I compared the two (Ch.3 Vs Ch. 29) and from what I can tell, it's not that he's less masculine or shorter, the artist just isn't spending as much time/focus on drawing out the muscle and the angles are a bit softer. His arms and general appearance are the same size, just not as detailed as before. It probably looks like it's effecting MC more cause he wears clothes that make the difference noticeable.
If we want an in-story-excuse, he's probably eating better and doing slightly less (≧∀≦)

Is it just me or has the black haired guy started looking less “masculine” compared to the beginning? He’s gotten shorter and his muscle mass has gone down (explainable). ╮( ̄▽ ̄)╭