When using "Import Over Sprite", index 0 from the palette isn't being considered as the transparency colour at all, making it impossible to use an opaque image for any small changes.
This isn't the case for the "Import spritesheet" function, which automatically assumes the background colour as transparent.
This can get really annoying for updating any existing sprites when you mainly use a tool that doesn't support transparency (such as MSPaint) and have to rely on a separate program to remove the background colour.
Sprite example used for importing :

Expected Result :

Actual Result :
