It has to do with how The Man views piracy. If a community takes steps to discourage what big businesses view as piracy, like romhacking communities that release IPS patches for copyrighted games, then they typically don't care. But they'll care if a copyrighted ROM is edited and released. I know that the EXE can't run without the other parts of the game and vice versa but because most people would consider the EXE to be the heart of the program, and because of legal crap, we kinda have to play by their rules. And we all know LEGO would say no to modifying and redistributing an EXE of a game they own the rights to, especially one that circumvents the copy protection.
But if you know how to do something like an IPS patch that alters the original file, then please, go ahead and do that.