Ok, sure. But is that only a visual change, or does it actually change how other characters perceive the MC? Because unless that change is acknowledged and the character is either referred to by different pronouns, or is perceived as something other than "male", than the tag is still incorrect.
The tag is being used as a shorthand to suggest the presence or option of a protagonist with some or all of both sets of sexual equipment. This has come up before, in this thread and elsewhere, and the tag is still there, so I can only assume that despite it not being technically accurate as per the definition of the word itself, the tag is still being used correctly as per the site's qualification.
If you need it removed or changed for whatever reason, you will have to 'umm ackchually' at the admins. At which point, provided you succeed, a new crop of people will likely pop up like dandelions in spring with screeches of "Y MC HAV BOBBS NOW THERE NO TAG WARNING REEEEE". Which, also like dandelions in spring, will be an absolute joy to deal with.
Before posting this, I did a little legwork (I used the site's thread search function). I saw that requests for separate and/or different tags went back to 2019, and the first thread I looked at had a site admin say they would look at it, but the work and Motrin required to maintain and enforce the implementation of all the tags required for all the current and future variations demanded of 'chicks with dicks' - to say nothing of 'dudes with boobs' - outweighs the benefits, so it was unlikely to happen. That admin was then suggested to be transphobic and what happened to that user may not surprise you. I laughed.
The best we can really hope for is that people look at the tags, see 'male protagonist', 'futa/trans protagonist', and 'transformation', and put the puzzle pieces together.
In other words, this here is just gonna keep happenin' aaand happenin'.