He's not transphobic for making those jokes, he's offensive, as usual.

Some trans people live in the same kind of la la land as religious or superstitious people, and mentally block out the inconsistencies between their self image and people's actual impressions, and rage at any suggestion of such an inconsistency. Both groups prefer to socialize with yes-men who reaffirm and reassure constantly. So when some of these people come out of their shell to aggressively reiterate pronoun compliance demands with "HER penis!", that's fucking funny. Even to someone who believed in protecting the right to transition and protection from violence and discrimination.

You should know where Gervais stands on the politics of this. He's likely more liberal than you. But he's certainly less protective of feeble minds. He's not interested in protecting anyone from ridicule. And neither am I.