Here's a short red column summoned at the console:
The only difference is that in the first pic, the sprite is being loaded direct from the iwad. In the second, it is a local copy of COL4A0 in the mod's sprite subdirectory. It was extracted as a PNG but has otherwise not been modified in any way nor is this a replacement definition with the replaces keyword. Even worse, replacing the copy with the original DOOM graphic lump makes no difference; in demo2.pk3 and demo2.wad the COL4A0 lump is a copy from the IWAD copied using SLADE.
I found this because I was using a "minor edits of stock textures" (as allowed by id Software) to fix the horizontal offset in COL4A0 which in the stock sprite, is too far to the left compared with the similar sprites. But the engine is doing this even with a verbatim copy of the sprite.
There should be no secret sauce that the engine applies to a sprite purely because it's in the iwad or not!
Is this a bug, or is there something I should be doing, or not doing?
(These sprites behave properly in the software renderer.)