I now add and remove sceneries directly using the Scenery.CFG file. I have also found one or two instances where the layer= number was the same for more than one scenery, one which caused a crash...
This enables me to shorten the turnaround time to activate or exclude ...
This has been my approach for a few years too, it's just so much faster to get things done, especially as my sim took a while to start up and I always started from a saved situation that was accessed from a desktop shortcut (to "previous_flight.flt") that could take even longer depending on where I last was.
I took the opportunity at that time to also align the scenery layer numbers with the priorities, so they were always in alignment.