I answer yes to all your questions.
I think there is no bug, but I realized that there was a "problem" when I made a room with a switch that launches a moving platform and the hero has to hurry To join it. To succeed, it is best to activate the switch from the side and this is difficult, much more than from the top.
I really invite you to test by yourself.
Yes, I believe you are completely right. I had a similar problem (or even worse) because with the sprite I made for Eldran (a custom hero), the pixels of the feet are in a lower position than for Link's sprite, which makes this much more noticeable. Actually I modified his origin to (12, 23) to decrease this effect. With my custom switches (custom entities) I decreased this effect even more, maybe because I use a different sprite.
I could be wrong but, in my opinion, the problem is not with the engine, since it checks the distances between the center of both bounding boxes, and that is done correctly. The problem is actually the switch image, which is drawn with a bad "angle of perspective" (at least, for the way the engine handles the bounding boxes); when the hero and the switch bounding boxes are centered/aligned one above the other the hero "does not seem" to the player to be centered over it. An "easy" solution would be to redraw the switch sprite, to make its angle perspective better when both bounding boxes are aligned, i.e., draw the small circular part of the switch lower (and smaller if necessary).