I could come up with a logical reasons for this, but is that really how the author wants people to read their femboy comic??
Obviously.
So, clearly he has
Klinefelter syndrome and just hasn't been diagnosed, meaning that he has two X chromosomes and one Y chromosome. The "code" that checks if the MTF transformation is complete checks for the presence of a second X, so because he already has one, it just skips over it like "oh, he's already transformed. That was fast." Similarly, the transformation back to male checks for the presence of a single Y, so because that was never removed by the initial transformation, the whole thing is skipped over again. And the check for whether or not someone is a valid magical girl candidate is just whether they have a Y chromosome at the time of selection, so having the second X doesn't get in the way of that.
And, honestly, this explains his unusually feminine appearance, too, as, per Wikipedia, "[d]uring puberty, KS subjects show less muscle mass, less facial and body hair, and broader hips as a consequence of low levels of testosterone" and "as teens, persons with XXY may develop more breast tissue." Like, seriously, you can't just look at those last three illustrations and think "yeah, its normal for a guy to look like that," especially with p8. Look at those proportions!! Those are obviously boobs on p8! Guys just don't look like that unless there's something else going on, and his appearance
just so happens to fit the description of Klinefelter syndrome to a T?? (Well, it's not like we've seen his testicles, but... There's also the thing about height, but Wikipedia, at least, specifies "by adulthood" for that.)
Like, I'm obviously not serious about this, but if this weren't an obvious fetish manga, I'd be tempted to think that this was intentional. It just makes TOO MUCH SENSE.