Yeah, like I said in the title, I found one interaction where the savegame editor does something weird:
Say you want to add the unused safehouses back into the game. You make the lines in gta.dat for the marker placements, as well as the other necessary things you need to make in the maps folder for the enex marker data (such as coords) So for this example, we'll use the LABIGSAVE interior, grabbing its coords. Basic stuff, yeah, I know, then it gets to the point that screws with the Savegame editor.
Next, you script the floppy disc pick-up to appear as well as the functions of saving that it provides. Now comes the fun part: If you save here, then use the savegame editor to start at a different location, it will always spawn you high in the sky above (at about 1000 for an x coord) wherever your last save was - so for the LABIGSAVE, it'd be above jefferson since that's where the interior is located. I imagine this is caused from the savegame editor not knowing where your previous position was, so it goes all crazy.
Also, another strange thing, a normal save I was using seems to not be recognized by the editor - the only "mod" I made with the save here is using the satchel charge glitch to get more territories in the game, but nothing else. Just doesn't accept these files, for some reason.
This isn't really a help thread (well sort of for the second part) but moreso just a strange interaction I've found. Thanks for reading this if you made it this far!