There is no point in reducing the RPM of VS pump below 800-1000 RPM. That is the most efficient speed and efficiency drops off with lower speeds. And yes, you should be able to lower RPM on the pump while running the booster although it still isn't as efficient as running a pressure cleaner without a booster at higher RPM.

How do I know I am getting proper skimming other than seeing all debris not making it in the Polaris ending up in the 2 pool skimmers (spa has none but overflows in pool)?
That's pretty much it.

Also, I serious doubt you need that much run time for your pump. Run time is mostly for removing debris from the pool. Generally skimming will occur within the first hour or two and after that, not much happens unless something else falls in the pool. So you are much better off with 2 periods of 2 hour run time and set the speeds for optimal cleaning. Adjust the pump run time based upon how well it keeps the pool clean. You will probably find that you do not see any difference at the reduced run time.

I hear some noises (sounds like small stones) around the 6-position variflow valve interfacing the filter: the equipment installers said this is normal due to the high water flow.
That is NOT normal and a good indication of cavitation so I would avoid running the pump at full speed. Backwash valves can cavitate under the right conditions.