Think it's pretty much guaranteed Kotone & Mei will be a thing unless author really pulls one out from under us. Kotone liked Mogu because it basically meant Kotone could project the desire for a same-gender relationship on a amab person, which Mogu was uncomfortable with for reasons which should hopefully be obvious by now. Mei basically gets all of the advantages of this with none of the disadvantages, plus it's no longer a projection because it actually would be a same-gender relationship.
That said Kotone is probably going to say some hurtful/transphobic things to Mei without realising it, before everything settles into place. After all one of the main themes of this manga is about how people in lgbt/gsrm communities can hurt each other unintentionally, and how to apologise for it and change for the better afterward. I think unintentional for Kotone because I doubt the author would write this development/growth arc just to throw it all in the garbage.