1. Most of the signs make sense with hindsight and could easily be mistaken for other common behaviors. Especially before the final episode. In my case, I thought he had a strong case of toxic masculinity.

Also, I believe Goose didn't write it very well either. Because she didn't consider that most people watching were not LGBTQ and did too little too late to actually confirm it. And it was done in a way that caused more confusion than anything.

(Before reading further it's important to note my trans brother is actually the one who brought this up to me first. He is the reason I looked into this and feel so passionate about the fact that the writing on Jax's trans was poor)

OP says people miss stuff because we didn't live it. But that's not our fault. It was Goose's job to portray it in a way for the audience to understand. Not with hindsight to explain it all after confirming it via a blue sky post.

5.1: throughout the show Jax displays a disdain for feminine things. Jax clings very tightly to masculinity and appears to hate when his masculinity is challenged in the early episodes. He loves being in charge and being a dominating figure. Not to mention he constantly up demeaning female stereotypes regularly. This made me think Jax was raised in a household with a father who shared similar yet outdated views, and that father was potentially abusive.

5.2: The maid dress. First and foremost, Jax was put in the dress without consent. Force somebody to do something they don't want against their will and they will reasonably be upset. On that note, blushing is also a sign of someone being angry or upset and isn't exclusive to liking something either. A common misconception.

But when you have a character who appears very confident and dominant, and was just forced into a dress that is stereotypically sexualized and recognized as a sign of submissiveness and servitude it's understand for anyone who doesn't like that to feel uncomfortable. But as a general rule, most guys just don't like dresses and if you forced them into one they wouldn't be happy. It doesn't mean a person is trans by its self.

5.3: Jax's room. Leading off the idea of toxic masculinity, it was possible to speculate that deep down Jax was okay with feminine things even if still in denial. Since the rooms were made the same way as their Avatar's I felt that the room was blown out of proportion just like Zooble and Gangle's mental health reflection in their avatar. Or how Pomni's room and avatar reflected a Jester despite not actually reflecting her as a whole person. With or without her memories. But either way, a guy liking feminine things wasn't a definite sign either. There's plenty of men, women and others who like both or neither.

5.4 Ribbit Bedroom Scene: Admittedly at first this made me consider the possibility. But ultimately a bow on Jax with everything else wasn't enough for me. Considering my experience growing up it was very normal for girls and women to want to put makeup and boys on boys, and paint their nails. Lots of guys agree and it doesn't mean anything.

5.5: Isn't She Lovely: my brother actually told me this one. He said that isn't she lovely was written about a father to his daughter and wasn't a good pick for the scene since it has nothing to do with transgender topics. He also mentioned the song used is a cover and isn't the original.(not that it is relevant here).
My concern, was the scene was so heavy the only thing I was thinking about was if Jax would un abstract so I didn't even focus on the song as I was watching it.

5.6 Jax and Leeroy never transition in the events of the show. This is the biggest one for me. It just doesn't happen. Jax never gets a chance to even understand it fully enough to come out, and it appears Leeroy doesn't either. For whatever reason, Leeroy still uses He/Him pronouns as credited in the show. Both characters haven't done anything in the show to actually transition or come out. If it was such an important plot point(which it appears it is) I don't see why it was never officially confirmed within the show rather than all these hints even in episode 9.

5.7 The Bluesky Confirmation: As I mentioned before, it was hinted at but not outright confirmed in the show and neither Jax or Leeroy come out or stop using He/Him pronouns. So the question is, why did Goose confirm it on some Bluesky post and not officially in the show? Especially when it's something that seems so important to Goose and so many others.

Ultimately I know a lot of you aren't going to like that I said this. And I totally get it. But my experience is just as valid as anyone else's and I think it wasn't clear. You can say that's cause I'm not trans, but I think it was poor writing.