Sorry for my late reply. I've been otherwise occupied and away from imgflip for a while.
You make good points here, kneez. The only problem I see with what you're pointing out, is that ultimately it's not possible to know with certainty what's in another's heart. So we usually have to go by their actions.
So, while I agree with the notion that a person could intellectually support people having equal rights, but still be prejudiced against them, without their negative actions to back that up, what have you got? If it's in someone's heart to be prejudiced against a trans person, then I think that usually their prejudice will come out in how they treat them, or their political views about them. Usually, but not always.
I did have a discussion with someone here on imgflip about being homophobic, quite a while ago, who claimed to be very religious. They used the old tried and true comment about God teaching them to love the sinner, but hate the sin. I've known people who are actually like that. I think they may be good examples of the people you're referring to, who can support trans rights, and still be transphobic. Certainly not the only examples though.