[bitwize]

Modification of software for your own use is fair use. This was established in Nintendo v. Galoob.

Take for example the DeHackEd Doom patch editor for old-school DOS Doom, which patched the Doom.exe binary to change player speed, enemy behavior, text messages, etc. in ways that WADs alone couldn't. You are free under copyright law to use DeHackEd to patch your own binary, and to distribute your patches so others may use DeHackEd to apply them, but not to distribute patched Doom binaries.

The same holds true for any game mod, really, and even those Windows installer editors which produce stripped down versions of Windows (like 98lite or the more recent Mini11).