The things you can complain about in fandoms is pretty much the same as what you can complain about in any kind of group mentality. Even the most oppressed of people can become just the type of bully they hate if they are in a group that confirms their bias and if they feel that their agressive actions are justified.
As for the trans/Lgbt side of this issue, I feel like what you mentioned here is a core actor in this situation. If you want to make a genderbend, go ahead. I don't really mind. But if it's an ftm man, make it an mtf woman or otherwise transgender nonbinary (who said genderbends have to be binary? There's a huge world of activism to be explored in nonbinary genderbends). Making the character not transgender in a genderbend will do two things...
It's no longer that character. The transgender aspect was a core piece of their identity.
Transgender people are constantly being fed a message when they walk through life. When they meet new people, when they talk about their experience, and more than anything when they seek healthcare in regards to transition. This message basically goes that cis people think that the thing transgender people ultimately want is to be cis. As if cis is this elite form of existence. Cis people either laugh at us or pity us for the fact that we will never be cis. Many trans people internalize this and end up believing that they will never be valuable or happy. Genderbending a transgender character into a cis person would either force this person into the gender they were stuck pretending so hard to be, or it would confirm the message i mentioned earlier. The notion that hey wouldn't it be so much better if they were just, you know, not trans.
We already deal with this when we seek medical help. The doctors basically want to either force you into a gender that aligns with your body, or they will try to make you change your body and identity to suit the binary opposite as well as possible. This is so that you can pass as cis. Because cis is the ultimate form of existence, right?
I'm not personally offended that some person drew a trans dude as a woman. It's a random drawing, it doesn't affect my life. I'm just telling you why some people might be offended and in which circumstance this feeling might be justified to some extent.
At the end of the day, fact remains that a hugeass attack on a person is neither okay nor productive.
...oh, and, sidenote. People keep complaining about how "YOU CAN'T EVEN JOKE ABOUT DIS ANYMORE". You do realize that dem old peeps were saying the exact same thing when joking about "killing n---ers" wasn't okay anymore, right? Just because joking about something was socially okay yesterday, that doesn't mean it didn't contribute to unhealthy shit in society.
I could go on for hours about this but let's make it simple: You can joke about trans things just like you can joke about aspects of any other group. Hell, I joke about my 1 inch dick all the time. But if you are doing it with mocking/cruel intentions, or if your entire punchline is "LOL IT'S A TRANS PERSON" or "WOW TRANS PEOPLE ARE DISGUSTING (See: Family Guy, the scene where Brian throws up for a FULL MINUTE when he realizes a woman that he had sex with used to have a dick)" that's a problem. Trans and gay people are tired of their entire existence being either a sin or a joke. We are also tired of people framing us as the most disgusting type of human there is, only to be called "triggered bitches who need to take a joke" if we protest.
Basically, laugh with us. Not at us.
Wow this post became long.
Oops.