I've thought about this in connection with Mozilla's strict policy about the Firefox name, in particular the problem it poses for Debian - if even a small bug or security fix is applied by anyone other than Mozilla, the patched program can no longer be called "Firefox". This of course is not how FOSS software normally operates. When software gets packaged in collections, be it Linux distros, the BSD Ports Collection, MacPorts, or what have you, many packages require patches to be applied to the vanilla upstream sources to fix minor issues. If everyone acted like Firefox and disallowed such patching, the FOSS world would have huge problems.
I think the tricky part is how to allow the above "good" third-party patches, without opening the door to the sort of problems VLC is experiencing. I'm not sure there is a legally rigorous way to do so. Certainly, Mozilla takes the position that all modifications are incompatible with the Firefox trademark.