Unwanted persistance and improper saves, Master section

.yes, I really do remove the plugins. The “Restore last setup at next startup” option in the settings menu for the Master Section does not restore the empty setup you leave, but the last plug-in chain you had put together. This does not seem logical to me, but is the way it works, consistently. Therefore the only way to start up with an empty chain is to uncheck that box.

What you describe here is not the way it is meant to work. And I can’t reproduce a problem here.
The last Master Section preset is stored in this file:
C:\Users\UserName\AppData\Roaming\Steinberg\WaveLab 8\Cache\Window Config\MasterSectionPreset.dat

Try erasing this file once, and reload WaveLab. Maybe it’s read-only by mistake?

The option in the Workspace menu for shared tools/Master Section is for DISPLAY ONLY

Yes. Hiding the Master Section does not mean it is not active (in the same way as a plugin: no window does not mean the plugin does not work).

-The “Monitor 16 bit dithering” selection in the Master Section settings menu is more than a little confusing to me. When unchecked, are you simply bypassing whatever dither you have in the dithering section, even if this dithering were some other value than 16bit?

No. If this is unchecked (the default), then WaveLab does nothing. It uses the Master Section as it is set, nothing more, nothing else.
If the option is On, then WaveLab reduce the level at the Master Section input by -48 dB, and raise the level again at the output. This is only to make “hearable” what’s happening at the low levels.

-It seems to me that the “Smart Bypass” in this section is always engaged in that you can’t disengage it

No. Make bit custom corrections, to make it obvious, and you’ll see this is not the case.

I am still hearing a difference in audio between a “hard bypass” and an empty Master Section

Maybe an explanation: if you don’t have any plugin in the Master Section, but have “Monitor 16 bit plugin”, then you have a process going on, and the sound will not be the same as a fully bypassed Master Section.
Other than that, I can’t imagine a difference.