It's more than that. A lot of manga will sort of keep the swapped as a girl for reasons other than the author "simply wanting them to be a girl and also dating a girl -- ergo yuri." It's more like, if they could figure out a way to make them both "a straight couple" while also "keeping the swapped swapped" and also not turning the girl into a boy (because that's icky, to some), they probably would. So, a number of TS manga will end on a very ambiguous note of "the boy might swap back to being a boy one day, either temporarily or permanently, for any number of reasons, including possibly so that he might father a child with his lover." Tensei Pandemic did this (though don't get me wrong -- it still ended yuri enough for my tastes and I was happy with it overall -- but it still could've ended even more to my tastes). Ayakashi Triangle did this (I think? I haven't finished reading it but I seem to recall hearing about it). It's very rarely ever okay in the eyes of TS manga for a swapped boy to just be a girl and love a girl and have that simply be the end-all-be-all of it. There's always some nagging downside to it or implication that some further gender rearrangement might be "necessary" for the couple's happiness or future plans or whatever. In other words, the yuri is often incidental, "functional," or simply "how it has to be," rather than the author specifically liking it.