I haven’t read the manga, but in the anime the only time I remember Makoto saying they don’t want to be a girl is when they say something along the lines of “I don’t want to live as a boy or a girl, I want to live as me”. They read to me as pretty obviously someone not done with their gender journey, with a lot of internalized transphobia. And judging from their reactions from people reading them as a girl, I’d guess they’ll end up transfem (whether girl or nb).
Makoto did also say that in the same scene, but I largely take the “I’m a boy” comments with a grain of salt, since much of that often reads as “I’m amab” or “I’m supposed to be a boy”. I’m also not sure the egg prime directive applies to fictional characters*, though I’d definitely be using he/him if Makoto were a real person, yes, lol.
*There are a bunch of reasons for this but one of them is that the nature of storytelling is that each person’s understanding of a story is a little different because no medium perfectly relays what’s in the author’s mind into our minds, so we each get our own personal Makoto in our own heads. Mine is definitely a girl (egg) but I don’t really fault anyone for coming to different conclusions (unless they’re for transphobic reasons, lol)