I don't know I haven't made a map or ported one yet.
I'm looking through the mission files now. Map_KitchenDark.zip/KitchenDark.mis uses the interior file "Add-Ons/Map_Kitchen/kitchen.dif" so it looks like you can call things outside the zip. As you probably know, Bedroom and Kitchen use the same terrain textures. Oddly enough, both Kitchen and Bedroom come with their own set of terrain textures. However, Kitchen Dark uses Kitchen's set of textures (and does not have its own set of textures, although for some reason Bedroom does). So I guess you can technically load terrain textures out of other files.
Skies still go in base/data/skies. You could probably get away with packaging the sky into the zip though. The sky would just be called ./resource.dml in this case. Actually, I don't think it has to be called resource.dml, you could probably call it sky.dml if you wanted to, because custom precipitation also appears to use resource.dml.
For some reason the tutorial map (it's expanded by the way, with information on how to make lights and vehicle spawns, nothing on events though) is loading its water out of base/data/water too. I don't know why, I think you could also package water textures into the zip if you wanted.
Here, you can take a look at the way a few of the zips are set up.
