Debatably Transgender BL

I thought this was about a woman who swapped bodies with her father but got married in that state. Sadly the wife is poofed out of the equation and the one the MC marries is literally the father in law.

Known to everybody on campus as a woman, takes jobs as a woman, refers to herself as a girlfriend... She just happens to have a penis! World's first transfem "yaoi" (het). You could also interpret them as nonbinary or... cis (probably the author's intention)
This is essentially a femdom futanari hentai with a yaoi label. I do not recommend it if you're looking for good trans rep or an insightful analysis of gender but it is a wild read

Not a BL but has a gay/bi male character. Many nuanced themes on gender so I would recommend checking it out if you're into that trans shit
I really love how this manga presents not just gender and sexuality but how complicated attraction is on top of being queer and defying societal convention. A very interesting work.

Very explicitly transgender.
It IS only debatably a BL though.
TW for trans mascs who are uncomfortable with being liked due to being perceived as a woman, there is an arc about that. However, it is left unclear if the man who likes the trans mc actually views him that way or if it is just his guilt complex. It is handled very thoughtfully. I highly recommend this bc transgenderism aside the characters are amazing and it's very sweet

Pretty much just porn. The argument for this being trans is pretty weak but there's an inherent transness to gender bender as a genre and this is one of the rare ones that isn't entirely a rape fantasy (*coughs*likeboymeetsgirl) unwillingly inhabiting anatomy that isn't "yours" is kind of transgendercore innit?

The main plot is a BL/yaoi but there is also an implied transfeminine character who never gets a happy ending. It isn't anything against the character due to the author's bias, rather the story has a pretty clear theme of the struggle of achieving happiness while being queer and the obstacles and sacrifices one must often surmount to get there. It's depressing , bittersweet, and thought provoking. I would recommend it I'm just giving a heads up for those that don't want to be depressed.