After doing a whole series of tests, the behavior of the Master section and its relation to menu items is a little more clear, even if I still feel that this new behavior is more than a little confusing and hidden:
-The Master section settings menu choice “Restore last configuration at next startup” behaves in the following way:
…When checked, it will, EVEN IF YOU HAVE EMPTIED THE MASTER SECTION, restore the last set of plugins and dithers you had in place.
…Therefore, the only way to start out with an empty Master section is to have this box Unchecked. This behavior is now consistent.
-The Options Menu from the Montage that chooses “Play Through Master Section” AFFECTS THE MONTAGE ONLY! A plug-in filled Master Section will still be active for the Files window.
-The selections in Workspace Menu for both Files and Montage windows to select the Master Section under shared tools is for display purposes only. In other words, the Master Section is always enabled and can’t, seemingly, be disabled for the Files section at all, except by emptying it (or using a Bypass mode). The Montage, as described above, can have the Master Section disabled by unchecking the “Play Through Master Section” in Options.
-However, having the “Play Through Master Section” unchecked (Options/Montage) is not persistant. It is always checked when I restart the program.
-I still hear a small change in the audio during Montage playback when I compare “Play Through Master Section” checked and unchecked, even with the Master Section emptied. I don’t like this, and want to find a way to guard against it.