I suspected the reacta scuff could cause more pronounced alterations, given it is scuffing the surface. I wonder, then, is it better to use something like the reacta foam, for example, after each use, and use the scuff after every other set with this cover?
Again, not rocket science.
Scuff puts on a certain surface, whatever that grit level might be (if applied exactly the same every time: amount of compound, amount of pressure, time applied, etc.; lots of variables, be careful.) If that's the surface you bowl with, everything is good. You can use it whenever.
If, however, you use a specific grit level, usually applied by an abrasive pad or other mechanism, then, whenever you use Scuff, you need to go over the surface with that specific pad to return the ball to its usable surface for you.
If you use a good, normal cleaning regimen, it should not be necessary to use Scuff very often, if at all. Good, deep cleaners, like the Lane Masters you say you use, Hook-It and Clean and Dull, will clean everything off balls that can possibly get on them. If you use super oil suckers, like balls with NRG coverstocks, you may want to do an oil extraction every 50 - 100 games, depending on the observed performance. You may not need to.
Along with cleaning, to maintain performance, surfaces do need to be refreshed regularly. A complete re-surface (if it's 500/2000, you need to reset the base surface to 500 grit and then re-apply the 2000.) should probably be performed every 30 - 50 games.