Anything like sun, clouds, or trees require overwriting stock files in the main Texture folder. Having a backup of that is a smart idea.

As for putting addon scenery packages on a sep. partition, that will work as long as you point the scenery library to the right folder, just like using the Addon Scenery folder. You can even use an external drive as long as you make sure it's plugged in and running prior to starting FS. If you start up FS and there's scenery missing, it will throw up an error. (Which is why you also never just delete an addon scenery package without first removing it from the library.)