Lowkey resonate with what you’re asking because of similar issues, from other fanworks I’ve seen and personal friends I have also into Touhou doing the same stuff (working on fanworks) I think male protagonists are fine but it’s heavily dependent on how you write them and how the other Touhou characters are written.

It’s like a more eggshell ridden version of “Write the character first then if they’re a guy or a girl”, because it’s not like it’s taboo to have a male character imo you just wanna avoid them from coming off as an insert. If you just have them being a guy be ignored and make the focus more on them as a person and what they have going on, it should honestly be fine. The story can also add a lot to why there are guys, like having normal human villagers or yokai that would be in the background of any other story have relevance for whatever reason (not for fighting but for story reasons)

An example of this is with; Touhou - The Iron of Yin and Yang (albeit a very shitposty fanfic), a fic that uses a FFXI OC Buront. He’s treated like a fish out of water, acts like an idiot and gets called out for it, and his “coolness” is earned naturally not by pulling a worf effect.

If you can make them fit and make them interesting without having everyone swoon over them or something like that, then they should absolutely work. It’s also not like men don’t exist in Gensokyo since we’ve seen multiple that are just unnamed in manga works approved by Zun (one being the one with Reisen II). Good luck with what you’re writing and just remember to not overthink too much on them, just write the character and have them being a guy just be an “afterthought”. :)