Well, I have absolutely zero experience in stage hacking, but it seems to me that the custom stages are no more than data files that contain information like which theme the stage uses, all the parts used in the stage, and those parts' respective locations. So unlike a real stage, custom stages are just packs of data arrays built into a playable stage upon selecting it on the SSS. Ergo, the extent of hacking custom stages is hacking the themes you can use to create them, and nothing more.
Of course, this could be completely wrong, since I'm no expert on the matter, but it makes sense to me (plus it explains why it takes so **** long to load custom stages)