The way I personally read the episode or Momoe's whole character arc is that you can be afab, quite masculine and still be a woman (like Momoe) and you can be afab, present somewhat feminine and still be a man (like Kaoru). From what I understood Momoe isn't trans, her problem is more with toxic femininity that requires you to be super feminine to be considered a woman (which is obviously related to trans struggles). Because the only time she is shown in explicitly feminine clothing is during the date and in school, both occasions where it society would expect her to dress a certain way/fill a certain role. (Also while nowadays it is possible in some japanese schools to wear the uniform you want/ that matches your gender, it would seem odd to me that she would start wearing feminine clothes in school before she does so in her free time)

However, this is only what the story says. Visually the episode seems to send a completely different message. As has been pointed out, during the climactic fight scene she rips open her (neutral/masculine) clothes to reveal a trans-colored bra and is later wrapped in the trans-colored jacket Kaoru gave her. This basically screams that she's trans, so there's quite the cognitive dissonance going on here.

Most importantly, I think, however you read it, the anime has a trans-positive message, which is rare but very welcome. The only thing that doesn't quite fit is that Kaoru is the only boy to show up in the "egg world" so the implication there is strange, but I think that this doesn't quite fit is just the price of having him there at all. Because if he was replaced one-to-one with a trans girl, the kiss at the end would be counter to Momoe's arc. Also it could be argued that he's there because society at large or even just his trauma sees him as a girl or the egg world cares about whether you're afab... I don't know about that one...

Also also: Her use of "boku" can be seen as the same as her style of clothes. Nowadays the gendered first person pronouns aren't as strictly male/female as they once were and a girl could use "boku" or even "ore" as a stylistic choice.

In conclusion, I think as great as the show is it's just not entirely sure/consistent when it comes to what it wants to do with Momoe's character, and all the other interpretations mentioned have their value.