Only for astralia, bahamut could still manifest in estalucia. Infact partita was going to call him through the shrine before he manifested without being called.
Astralia needed lyria to be in estalucia since her manifestation is fully tied with her
All Shrine Priestesses are conduits of Bahamut. That's why Partita was specifically brought by Repti to hitchhike with him with Captain
They are all granted power by Bahamut. And Partita has no way to resist this.
It's more more likely, they need to consume each other whole not just through powers and my guess is that the clone returned again not the main form of the omnipotent.
But I guess that kinda works for now since it could probably be because of plot reasons
Yes, it is just the Clone afaik. But that is more than enough, since the Physical forms are just a manifestation that can channel their power
Also, bahamut and astralia has always being inside lyria and they never ascended even though they could one way or another consume each other inside.
Proto-bahamut actively resists Sky-God. Only Vyrn really could do so, but in the Bahamut FLB. Proto-bahamut from Lyria saves Vyrn from Sky-God.
Astralia is inside Lyria, but she has to convince Lyria to grant control of her body, and she also needs Lyria to awaken the Blue Will Factor. (Astralia on her own can't do this)
Not to mention, both God wants to ascend the Throne with a plan in mind on how they will do it. and how they will lead it afterwards as Omnipotent
For Astralia, she specifically needed the Conduit who has the Blue Will factor so she won't have issues dealing with the Blue Will's interference.
For Sky-God, he didn't really need much. He just needs to reach Estalucia while also finding a way to deal with Rel
Since Rel basically can prevent them from accessing anyplace in Estalucia and was even Hostile when she sensed Sky-God in Partita, and it was only possible later when Rel's control in Estalucia was compromised by Demiurge, and is about to collapse. Astralia used this as a reason to convince Lyria that if she defeated Rel permanently, she could undo the Laws of the cycle of Life and Death to bring the crew back