Why wouldn't it be OK? There shouldn't be a problem; although I haven't progressed beyond Windows XP, I've made WW2 Pacific, Korea and WW1 variations as well as a couple test variations (changed the cfs.exe name accordingly*) and all work with the parallel install.

If one does this, it's best to copy the cfs.cfg from the first 'settings' complete install and rename it accordingly or else have to redo the settings again for the newly-named variation