The problem I have with her being homosexual is that it just flies in the face of the story they tried to tell.

Two characters who don't exactly know how the feel about each other but spending time with each other on a shared adventure begins to cause a closeness to bloom. Ambiguous but also fairly straightforward.

To say "nah, it's nothing, she's not into that" is stupid and killing the narrative. It just seems like one of those dumb rug pulls where the author is like "you THOUGHT you knew, didncha?!"

Yeah, I thought I knew, because that's the fucking allusion you were making. Don't piss on my shoe then tell me it's raining.

I have raised that as an issue with these two.

They could mate and have kids but where would that leave their kids? They're stranded in a reality where they're the only members of their species.