More details about persistance and Master section

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.

Having learned this rather odd set of behaviors, I would like to also understand how some other things work:
-How does the Master Section settings choice “Monitor 16 bit dithering” work? When unchecked, does it simply bypass your dithering choice in the dithering section?
-I would like a more in depth understanding of Smart Bypass, and for someone to look at how this is possibly impacting monitoring with the Mastering Section apparently always in line.

See my elements of response in this thread:
Please don’t make 2 threads about a same subject.

The “Play Through Master Section” defeat switch does, actually, exist in the Files window as well, but as a button on the info bar below the file screen, not as a menu item…which I just noticed is a duplicate of the same button in the Montage. Pressing the button results in a flashing warning. Although I would contend that this is maybe the reverse of how things should be, at least there is a way to completely bypass the Master Section in both windows…once one realizes this is your only option.

The relationship between the Options Menu item in the Montage and the button to do the same (i.e., hard bypass for the Master Section) is logically screwy, by the way. While unchecking the menu selection will depress the button and give you the warning, depressing the button will not uncheck the menu item. This leaves open some logical problems in the programming as a possibility.

That being said, I would still like there to be an examination of all Bypass modes within the Master section to understand why I hear a difference with an empty Master Section in play compared to this “hard bypass”…It seems to me that Smart Bypass is always engaged, in that you can’t turn it on or off, only select its path.

There are two obvious problems I am trying to address here:
1)The murkiness of the status of the Master Section at all times.
2)The alteration of audio passing through an empty Master Section.