Last time I checked the only thing you 'vis' are maps. You don't 'vis' pak files.
The pak files are convienent ways of 'pak'ing a whole bunch of files without having to dump it all over a directory. As long as your directory structure in the quake dir isn't all hosed I don 't see the problem. Besides work for a completely seperate gametype would probably be done under a different folder than 'id1' which all the vanilla quake1 stuff/pak files are under.