Can you at least quote the part of the EULA that forbids that instead of just claiming something that isn't even true:
That has nothing to do with the EULA, it's the basic principle behind every law: If something is obtained illegally, it cannot be used legally - no matter if stolen goods, police evidence gained without observing the rights of the suspect or in this case the internal (and secret) information about how to access and change the engine, that can only be obtained by reverse engineering.
If that were not the case, the first part of that EULA-point would be useless and not enforcable, because everyone with the knowledge could then reverse-engineer the software, write a patch and simply claim that the patch had been found on the internet.
The only way to allow that is for Enterbrain to grant the user the licence to modify the engine - and since you're asking for proof, please point to me where in the EULA does Enterbrain grant that ability?
1. ENTERBRAIN grants to Licensee a non-exclusive, non-assignable, one-time-fee license to use the RPG MAKER 2003 SOFTWARE for the purpose of creating, playing and distributing games and projects created with this software. User shall promptly register SOFTWARE before its use.
I see nothing indicating that the user may modify the software itself there.
And yes, a similiar case about Ace had been discussed internally a while ago - the information to call functions in the close-source DLL of Ace was never made available in public, so any script using that information is illegal, even if the information was gained from the internet and not by reverse-engineering of the scripter himself. Otherwise most of the copyright laws would be voided by now due to the internet-distribution of scanned books...
However, Enterbrain and Degica might decide to ignore the use of some specific patches - like they decided to ignore the use of a reshack to change the game.exe's Icon for Ace-Games, even if legally that is breaking the EULA.
The reason why this entire discussion has gone on without a (public) answer by any Degica-Employee is because the only people with the authority and knowledge to make and publish such a decision were unavailable during the weekend.
But there will be such a posting to clarify that as soon as that decision has been made and translated into the legalese language. (and no, I don't know what that decision will be, I only know that it's been discussed at places where I have no access)