A trans tag isn't necessary for MangaDex. According to MangaUpdates, there are less than 50 series where there is a trans protagonist and less than 200 series where there are transgender characters at all. Tags on MangaDex should be both useful to the reader but also applicable to a large number of series for the sake of efficiency.
https://www.mangaupdates.com/series.html?category=Transgender+Protagonist
https://www.mangaupdates.com/series.html?page=1&perpage=100&category=Transgender+Character%2Fs
As for fixing genderbender, splitting it between Genderswap and Crossdressing would be better for the reader. Genderswap if the character transforms/becomes a different gender than their norm, and crossdressing for guys/girls dressing up as girls/guys. The 50 or so series where the trans protagonist is a main detail wouldn't apply to either crossdressing or genderswap, which isn't that big of a deal to have excluded. Least it's not genderbend (which I still say only exists because it rhymes, it's a dumb overly general term when defined that can be applied to way too much unrelated content). If someone wants to find series that involve transgender characters, they can use MangaUpdates or other resources.