I think this is a totally different issue, those come from the approximate modeling of the original game, some have cracks like that. Most of the time it was fine in the original game because scenes were rendered in 320x200, but the cracks are perfectly visible with modern resolutions.
Again this is an issue with game data, approximate modeling again.
Talking of that, blending 3d and 2d objects is a trick and will always look wrong under some angles. To compensate, the heights of 2d objects (treasures, torches, stuff on tables,...) must have been set manually to look good under the expected viewing angle, and some tweaks that "looked good" with the original engine may look weird in a newer engine.
Mind you some heights are totally wrong even for the original engine! They're a few famous obviously levitating treasure piles in cabinets and torches in mid air.