Yes, you can ignore the bold statement. That's only needed if you use the moodlemobile2 repository. We run gulp in moodlemobile2 repository, and then we copy the build files to the moodlemobile-phonegapbuild repository. Since you're already modifying the final files you don't need to do that.
So yeah, there's no need to fork the moodlemobile2 repository.
Cheers,
Dani