Actually, it appears that whatever bug causes the enemy sprites to be incorrectly offset 2 pixels above their hitbox does not affect scripted enemies at all. A scripted enemy's sprite will be correctly centered in its hitbox without me having to define anything about its position.
This means that by simply entering a number in each enemy's editor I can convert them from default enemies to scripted enemies, which will fix all their positions and will also be forwards-compatible if that bug is corrected!
Yay for good news!
EDIT: (this offset was one of the first things I noticed back in '09 http://www.purezc.ne...=43287&p=612670 I never imagined I would find a solution for it! Incredible!)
Edited by Cukeman, 21 July 2016 - 04:46 AM.