Trans folks have been getting targeted heavily by the right for years now. They can be represented separately and the overall pride progress flag can also be present considering all of the other groups contained within and what the right says about them as well. Two things can be true without detracting from each other.
I think the flags serve a purpose almost like some form of heraldry when interacting in-group, as a shorthand way to share identity.
But as an outsider, I'm not going to keep track of every variant. I'd prefer there be one generic flag used when presenting to a general audience that is meant to encompass the entirety. And sticking with it. Maybe there already is one that is preferred?