For this I think it depends. When it comes to the Crimson Butterfly ending I think Chou suits the game better. The cow bell instruments at the beginning and the way the music gracefully picks up as Mio is running up Misono Hill and the way the song goes full blast as soon as the sun rises feels just right. It feels like the whole ending was timed just for it.
I think Chou fits better as the ending song rather than the theme song. Kurenai feels more like the theme of the entire game because it covers Mio's perspective and optimistic hope in restoring her and Mayu's relationship in spite of all the odds feels better as the games' theme song because that's the goal of the main character. The song has a really magical and beautiful feel to it because of the sparkly sound in the song as well as the violins just giving off a sense of "this is a very kind good natured person" and fits the whole theme of their relationship being something that you want to see fixed despite the problems Mayu has caused to it. Kurenai feels more suited for the Promise and Shadow Ritual Endings as well as the overall theme of the game, while Chou feels like it's better suited as the true ending theme of the game.
That said I really do like the way they symbolically have Chou turn into Kurenai by having them overlap with each other in the Crimson Butterfly Ending. It really fits with the song changing from a butterfly trying to fly with only one wing, into the wing of the butterfly trying to rejoin with its other half.