The film proposed either Biollante's spores going into the high atmosphere or Mothra flying into space with some cells stuck to her claws as the origin. Traditionally, fans favored the Biollante origin. The cited reasons are
- that this is the origin brought up in prototype treatment for GvsSG, Astrogodzilla
- the Biollante origin is mentioned in some early merchandise like the Treadmaster toys
- the two both have tusks on the sides of their heads
- both fall apart into energy particulates after death
AstroGodzilla was a story treatment with a fascinating development history, especially in light of it essentially being Toho treading water as the previous plan to end the series in VsMechagodzilla2 was scrapped as the American remake was in limbo. Originally, as many know, it started out as a Ghidorah script with a more showa-era like Emperor Ghidorah to appear. This appears to be a recycled idea from further back in development, where it was to be that the Heisei King Ghidorah was engineered from the remains of an actual alien Ghidorah and the monster we saw in 1992 was the Futurians essentially making a more controllable clone. A lot of Emperor Ghidorah's "DNA" if it were still wound up in AstroGodzilla.
Several of the concept art pieces for AstroGodzilla are still quite Ghidorah-like (and to be very fair, some are quite Biollante-like)
The choice to make it a Ghidorah fell through due to Yamato Takeru having the multi-headed Orochi, and there was a worry it be a bit same-facey having both films come out relatively close to each other. Still, AstroGodzilla remained very much an expy of Showa King Ghidorah as a spare faring, planet destroying monster which had wiped out several civilizations. Mothra, privy to this, sent back the warning before joining in herself. In fact in a weird way if you squint at it, GvsAstroGodzilla was something of a soft-remake of Ghidorah the Three-Headed Monster with Mechagodzilla/Moguera substituting for Rodan.
It is notable that the Vs. AstroGodzilla treatment, far as I can tell, makes 0 mention of Mothra as a possible candidate for AstroGodzilla's creation. In fact given it had been active and destroying planets for several years, it being Biollante who was the origin makes a lot more sense as a start. But, this isn't the monster we got nor is it the film we got. We didn't get AstroGodzilla, we got SpaceGodzilla. And more changed than just the name and general look.
And a big difference in the final film is, in both the English dub and Japanese original, SpaceGodzilla hadn't seemed to devastate any other planets thus far and was actually making a beeline straight to Earth. The echoes of Showa Ghidorah are much more subdued and the implication is that SpaceGodzilla is substantially younger than the prototypical version and hasn't had as much time to do such things. This makes more sense if SG was a byproduct of Mothra as she was in space far shorter than Biollante was.
Additionally, it reinforces why Mothra would be privy to this but couldn't turn back to help specifically if SpaceGodzilla was, metaphorically and literally, born yesterday. There was no time and that asteroid had to be diverted, so the best she could do is send the Cosmos' message as a Hail Mary to Miki and warn her.
But what about the facets of SpaceGodzilla that seem to line up with Biollante?
- that this is the origin brought up in prototype treatment for GvsSG, Astrogodzilla
-Potentially irrelevant as this does not reflect the final film
- - the Biollante origin is mentioned in some early merchandise like the Treadmaster toys
-Likewise, as on top of this many of the toys coming out abroad were beating the films by years and only VsBiollante had a stateside release at the time. It also could be a case of this being something changed later into production in some instances and the merch had to be ready soon.
- - the two both have tusks on the sides of their heads
-Virtually all of the Heisei antagonists have that, it's just a design quirk of the era. Plus Destoroyah has them and it was at least partially incorporating Godzilla genes into itself to make the final form, so it stands that Godzilla always had the genes for cheek tusks. Additionally, SpaceGodzilla's design came from SuperGodzilla whom had such a trait alongside the head crest and bit shoulders. Design development wise, it would have had the tusks regardless of origin.
- - both fall apart into energy particulates after death
-So did Rodan to be fair, if in a different manner. Additionally we saw similar particle effects off Mothra so this similarity is not quite exclusive.
Mothra also was much further out into space than Biollante ever got, meaning she had a higher chance of carrying the cells a longer distance for some to break off and accidentally wind up getting warped away. Mothra being responsible also adds extra thematic weight to the events as she caused this coming calamity and now, ironically, the very being she had to fight her hardest battle against is the best hope for planet Earth to survive. If one wants to get symbolic, the posters for the film practically look like she is anointing Godzilla as the planet's protector in her absence.
But there is in-universe another big reason why Mothra makes more sense. Remember those Futurians and their debacle? Now this is entirely in-universe justification as obviously the filmmakers were not planning GvsSG in 1990-1991 during Godzilla vs. King Ghidorah's development cycle. Emmy Kano stated that in the actual future, Godzilla never destroyed Japan. Why is never exactly clarified, but one can presume the most frugal explanation is that the Godzilla that attacked in 1984 and then battled Biollante in 1989 never recovered from the anti-nuclear bacteria and remained dormant in the ocean for centuries. Other possibilities is in the future they finally did find a way to kill him, or Godzilla never attacked again for any number of reasons.
Presumably the meteor strike from 1993 still happened regardless. That, combined with environmental destruction, woke up Mothra and Battra. The two eventually battled it out with no Godzilla interfering and given mankind was not substantially damaged, Mothra must have won again by either being forced into destroying Battra again or beating him down to stop. With Battra either dead, incapacitated, or pacified; Mothra (either with him or alone) sets out to stop the incoming asteroid that'll hit in 1999.
Here's the crux however. SpaceGodzilla in the film was able to go toe-to-toe with MOGUERA (whom is an upgrade over Mechagodzilla) and a post-double power-up boosted Godzilla, and win against either 1-on-1. Even with less monster attacks to damage Japan, G-Force or some equivalent agency would not have the firepower to stop SpaceGodzilla if they attacked in the Futurian timeline. At best they'd have another Super-X on call, but given this would be a year earlier and not have any Futurian technology to reverse engineer, no Super-X3. Even if they had an X3 equivalent, I don't see that cutting it given SpaceGodzilla's raw power, lack of easy to exploit weaknesses, and ability to heavily damage electronics. Even if Mothra turned the ship around and hauled herself planet side as fast as possible and even if Battra was still alive to help, I don't see a double moth + maybe a Super-X2.5 being enough. Not when it took G-Force's most powerful mecha made with future tech and a multi-powered up Godzilla giving it their all to win.
If SpaceGodzilla exists in the Futurian timeline, humanity loses. SpaceGodzilla would arrive planetside with nothing that could stop them before they could set up their crystal fortress. And once that is set up and it starts expanding into the planet, something easily forgotten, it's game over. You ain't uprooting them then. Not easily and certainly not in a manner that would go unmentioned by Emmy. Production wise the reason she never mentioned SpaceGodzilla, Mothra, or anything after GvsKG was simply because none of those films had been made yet. But in-universe the only explanation is that SpaceGodzilla never happened. No SpaceGodzilla also explains why Destoroyah didn't become as big of a threat as they did in the core timeline of the films. If SpaceGodzilla arrived, Destroyah might have either never been released to begin with by development in Tokyo bay, or SpaceGodzilla sought it out and destroyed it before it became a problem.
No SpaceGodzilla means either
- A - Development happened differently and Destoroyah never got released to start growing
or - B - Destoroyah was released but was defeated before it could reach its final stage, as there was no Godzilla to copy the DNA of to make the endoskeleton (the explanation for why the final stage is much bigger and looks different)
+ 
= 
This also makes sense of some of the seemingly supernatural abilities SpaceGodzilla has. If Mothra is, essentially, magical maybe some of it 'rubbed off' so to speak?
Now there is a way Biollante could still be involved, and that would be if some of her stray G-cells were in the high atmosphere when Mothra flew through them and unwittingly carried them. In this way, both were responsible. Why didn't this happen in the Futurian timeline? Could be Mothra managed to beat Battra quicker due to no big gray Goliath charging into the fray to complicate things and just by happenstance, didn't fly through Biollante's spore cloud due to leaving at a different time.
