SS just threw it out there to the wind with no explanation so I reinforce what he said with a little bit more info.
It is my hope that at some point we can divorce ourselves from id Software using our modified version of quake 2. In order to allow folks to play WF Fusion without owning quake 3, we need to get all the media owned by id software out of our software. Most of that we can do ourselves but some of the hardest work will come with removing stock quake 3 textures from maps. At some point the plan is to go through all our maps, using the official sources from WFA 3.5 (or newer versions if they have been updated by their owners) and remove/replace the baseq3 textures (if any) that were used.
So that is why he said try not to use baseq3 textures. We want to be able to get out from under quake 3's licensing restraints but in order to do that, we can't use any of their stuff.