There is no proof in the current storyline to support that. It is only theory based on the Phoenix Blade gaining power from lost life. Gaining power does not automatically mean restoration of life. Also Phoenix decided not to return to the mothercrystal to be reborn, so we have no idea what would happen if she did.
We have no idea how Phoenix joined herself to Sel'theus. There is no point in the story that says Phoenix is bound to Sel'theus. We just assume that because they are combined and as with other storylines, not all fusions are permanent. Square-Enix has lots of room to work in a Phoenix storyline. They haven't painted themselves in a corner as you're making it out to be where it's impossible from a lore perspective. All of this is player speculation, not story related fact.
If Bahamut was completely untrusting of humanity in the way you are saying, he would have continued to destroy humanity to save Vana'diel, not stop after Phoenix countered against him on the Airship and certainly wouldn't have stopped after fighting him in the Quest, Storms of Fate. Which is the last story related Bahamut fight. After you beat Bahamut he says the following:
Then Bahamut gives you his whisper which is a fragment of his power just like all the other avatars, only difference is you can't choose to apply that power to Summoning magic. I don't think it would be a begrudged pact, because someone who completely distrusts your motivations and capabilities wouldn't attempt to motive you, give you a portion of his power and stop trying to destroy the world which he could have easily done.Originally Posted by Bahamut


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