I tried to apply an edit to the ROM where the only change was randomizing the starters and this causes the game to freeze up, so that confirms what was already mentioned above. If the CRO editing tools can't be used without having the game freeze up, then these tools should be disabled in pk3DS (at least until it's possible to avoid a game freeze from having an edited CRO).
The randomizer which I originally attempted was recreated again with all of the edits I used in my first try (which freezed my game), but without the starters being randomized. This worked just fine without causing any problems, so I now have a working randomizer.