One City that doesn't get mentioned much here is Tübingen(~70k) in the south. Its pretty much as liberal as Berlin, probably the most accepting city under 500k population in Germany. It is ridiculously beautiful with a huge old town, and as someone who is queer and spends time there often, it feels very safe. The queer community is huge because there is tons of students. It has amazing City Planning / Cycling Infrastructure / Public Transport, and the surrounding nature is beautiful as well.

Disclaimer: I'm not trans myself. My experience/opinion is formed by listening to my trans friends and observing their experience.

Berlin is largely leftist with some anarcho spaces. Trans acceptance is mandated entry requirement. I'm sure some ahole wiggles in occasionally but I've seen others get very vocal and kick them out immediately. I would say it's an accepting place with several social events geared towards the LGBTQ community. A friend of mine is from the US too and she came to Berlin because of the issues she faced in her home country as a (trans) woman. It's been about a decade since she got here. I can find out about some forums, spaces you can talk / ask questions in. I don't want to presume the details and speak for the trans community. Shall I look into it and pm you ?

That is 300% the stereotype of Berlin. But it's true. If you like to be surrounded by leftist, queer, vegan people and waiters that speak english better than german: Berlin is your place.

Maybe look up where to live. You said you like a more rural place... Many many other people also like to live in the outskirts and surrounding areas of Berlin. But it's a bit different from other rural areas. I think it's called the "Speckgürtel".

Also i'd like to mention the city of Cologne, which is known for being queer.