I'm pretty sure he was vaccinated. He did criticize the piss poor messaging during Covid, i.e. claiming the vaccine would keep you from getting the virus entirely, which was never true, and harmful to the effort to get people vaccinated. He made a lot of fun of incoherent mask rules. If you watch his documentary, Religulous, you'll see that he's actually anti all religion, not just Islam. As far as being a transphobe, I'm not like a huge fan or anything, so I don't see his stuff all that often, but he doesn't seem like the kind of person to care from what I've seen. That said, his fawning over Elon in particular made it impossible for me to take him seriously, along with his compulsive shitting on millennials and Gen Z.
Pre-Covid he had a lot of whacky health ideas and thought that healthy vegan eating would solve most diseases. He didn’t like the idea of antidepressant meds, and some others.
He claims to be against all religion but it’s indisputable that he definitely doesn’t criticize them equally. He singled out islam repeatedly for years and says democrats should go along with Republican Muslim-bashing. Even though he claims to be an atheist, he defends rightwing Jewish extremists in Israel. He hates Arabs pretty explicitly and got in trouble for using the N word.
His irrational defense of Israel is another reason I stopped paying much attention to him. I can't speak to the rest because frankly I don't care enough about him to go verify everything you said. I remember him make fun of foodies a long time ago but I've never heard him do the vegan health thing. I have also heard him say the left needs to stop the weird fetishization of body coverings for women in many Muslim societies, which I agree with.
He absolutely does not hate all religions equally. He repeatedly defends the rightwing zealots in Israel and all their abuses because he hates Muslims so much more.