Unwanted persistance and improper saves, Master section

-The “Play Through Master Section” menu choice I refer to is at the bottom of the Options menu that appears in the menu bar for the Montage section (Options in File/editing section are different)…I consistently uncheck this before quitting and saving, and it consistently is back on when I reopen the program.

This option is not a global option. This is a per-file option. It is meant to be temporary used, hence this is not persistent.
If you want to bypass the Master Section always, click on the bottom right button of the Master Section. This is persistent.

After emptying the Master Section and making sure it is disabled in both the Montage and File windows (having it in one and not the other is a completely new behavior, by the way, and does not logically follow the “shared tool windows” concept from WL7)

Wrong. This has not changed as all compared to WaveLab 7. There is a single Master Section with a single plugin chain.

then saving, exiting and reopening the program (with the “restore last layout” option and with the similar option checked in the Master Section settings menu), I consistently get the old plug-in chain GUIs from the Master section displaying over the Files section window with the Master section itself sitting loaded in the Files section window

Normal, no? But BTW, a “layout” is not a plugin chain. This is completly independent.

but the option for the Master section being unchecked in the Workspace menu for the Montage section.

What option?

-With the program open, I clear all the plugins from the Master section and close it out…but the difference in sound remains between having the “Play Through Master Section” checked in the Options menu for the Montage compared to when it is unchecked…With today’s fresh ears, it seems that what I am hearing when it is checked might actually be the Master section with the restored plugin/dithering chain that I keep trying to eliminate…even though the bit meter is displaying 24 bits

Hmm, your description is not very clear. Do you really remove the plugins, or simply hide their window (in this last case, the plugins are still active). If you clear the plugins, for sure they are not used anymore.