FF6 Steam Version

Are those changes made in the ROM or in the exe? Well a file connected to the exe anyway?

I actually just resized the monster on its sheet. Monsters all come on a 256x256 individual sheet, I just scaled the leafer. The obb once decompressed contains 4000+ files, a lot of them being graphics you can open right away with Gimp. They have a 256 color palette, even if the leafer use roughly 50 colors he has a 256 colors palette (most of them being black). The pink background must always be index 255. Cropping and pasting the leafer to a new image lose that palette because even if the new image is indexed, Gimp will make some sort of optimization, reducing the palette to least colors, like around 50 for this example. At that point, you can't have transparency because you lost your index 255.

And while it shouldn't have any different results, what happens if you do that to a Narsh guard and fight them while on mtek armor?

I'm confident it will have the same result. There's no VRAM issue here I think, though it should be tested to be 100% sure.