The RM2k3 EULA and this jam's rules are two separate entities, so I want to comment a bit on the former:
The Rm2k3 Maniacs patch, as well as several others, are actually perfectly legal and EULA-compliant! That's because a few years ago RM2k3 got an EULA update that, to some extent which I'm not equipped to confirm, allowed users to create and use engine patches. I think it may even be the only RPG Maker engine where you can actually do that! You'll definitely have to confirm with a more reliable source, however.
Once again though, engine EULAs and competition rules are different entities, and KOMODO (or anyone who hosts a game jam) is entitled to permit and disallow beyond the restrictions of each RPG Maker's EULA.