The large circular bullets Orobas shoots out directed at the player during phases 1&3 were the only time I felt like the hitbox was actually a bit larger than the sprite. Everything else was more or less me feeling that it was odd that everything was as it looked. While on bullets I just remembered that the start of Sarcoph's final phase is awkward. It's probably just a matter of transition though because even though the saws spawn in instantly and start orbiting around I think at least their hitboxes don't come in for a while (until they start spinning?).
The only instance of being confused at the height of things I think was the area with the 3 stalls and the treasure chest, and it was when trying to jump to the outer walls. This was only because the path from the treasure chest felt like it was leading somewhere so I tried for a while. Everywhere else it was fine, just think it could read a little better.