Yeah, “realism” generally tends to be a pretty poor excuse for portraying bigotry, for several reasons. As has already been discussed, including bigotry that only minority players will actually even be aware of, let alone be affected by, feels almost targeted at minority players, even if unintentionally.
As a second point, even the most historically accurate stories on this site are going to be taking some liberties with the actual history, and the majority are not trying to be historically realistic. So why add real world bigotries to a world that’s not the real world, unless you’re writing the story specifically about bigotry (and if you are specifically writing about bigotry, I’d suggest either not writing it as IF, or using allegory instead of actual real world minorities)? If you’re writing a medieval fantasy, in which the main religion isn’t Christianity, do you really need bigotries that only exist because of Christianity?
But more than that, often “realism” isn’t actually realistic. For example, medieval Christianity wasn’t even that homophobic. Sure, the Bible spoke out against homosexuality, but for most people that was an issue between the individual and the Church, and unless you were unlucky, you’d generally be allowed to live your life in peace. Heck, the medieval Church even had special “brotherhood” ceremonies which would allow pairs of men to essentially be married. (It was almost certainly not intended for gay men, but it was definitely used by them… 
) It’s also worth mentioning that a lot of other historical societies worldwide were far more accepting of LGBTQ+ people, including Ancient China and Japan, and many African and pre-Columbian American civilisations. The only reason that people see historical cultures as homophobic and transphobic is due to the fact that the most homophobic period in Europe’s history is also the period when Europe decided that it wanted to own everywhere else. 