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)