OK, someone pointed this out to me:
<http://www.fedora.us/wiki/RepositoryMixingProblems>
Join us or we'll start reproducing your software in your place anyways.
I don't think that is what they are saying.
I think what they are saying is that their may be conflicts with their repository if you use someone elses as well, and that is a point worth considering.
That doesn't mean you can't use other repositories, it just means there might be some packaging conflicts you have to resolve (by telling one repo or the other to ignore certain packages).
I will say that I specifically do not like the fact that some of the popular repositories out there offer packages that REPLACE Fedora Core packages in the same repository as their add on packages - they really should separate those out to a different repository so that users like me who want to think long and hard before replacing a core package won't have to worry about that. Fedora Extras does not replace Core packages, it is safe to use. When it is available ;)