No, you donĀ“t. The extracted files have a higher priority than those in the .pk3 archive.
Unfortunately I have no experience with this terrain settings yet. So I cannot tell you how to find out which textures need to be defined right now. Maybe we have a script for this? Mattn?
The tex_buildings/floor017 texture (grey tiles), which is defined in terrain.ufo line 532 is used in the bungalow map.
The tex_nature/grass001 texture, defined in line 8 is the grass texture in the pipes_const map.
If you try those maps in Skirmish, change the parameters in the terrain. ufo and try again, you should be able to figure out whats going on. But remember you need to restart the game after the changes to make them work.
Any help with this would be very much appreciated, so, whatever happens, please report your findings.