I discovered some things after my initial post. I have a tl;dr at the very end that I think paints a better picture.I'm on 3.5.8698 and using Windows 10, and I am having trouble implementing exceptions for the auto-organizer (or I'm at least having trouble understanding how it works). In general, I want my files to be organized as <Album Artist>/<Album>/<Disc-Track#> <Title>. In this example, I am trying to organize an album so that all of the tracks go into the artist folder instead of an album subfolder (i.e., <Album Artist>/<Disc-Track#> <Title>). When I added the exception, nothing happened. I turned off "auto-organise" and used "Organise Files..." under tools, and it did work.

I turned "auto-organise" on again, and it seems that the rule is still being ignored.

It doesn't automatically move the files back to the album subfolder, but it does when I press "reorganise." Is this the intended functionality? After reading the wiki and several posts here that were related to this issue, I was under the impression that the reorganise function is supposed to follow the exceptions. I would like to have the option to still use the reorganise function without having to go and uncheck every song that I want to deviate from the primary template (I plan to do this with several albums). All files used in these tests were located on the M:\ drive, which is the drive on which I store my entire library.
For more context: I have the album CON.FLEX by CON.FLEX, and I am trying to implement an exception to the auto-organizer so that the artist and album folders are organized as "CONFLEX," because having a folder named "CON.FLEX" creates problems with Windows Explorer. However, I cannot get the exceptions to work. I tried this with a different album to confirm that it's not just a problem with the band name, and I couldn't get any exceptions to work period (e.g., I want the album field for "When the Pawn..." by Fiona Apple to contain the entire album title, but I want the name of the folder it's saved to to just be "When the Pawn" so that it doesn't create errors with the filename length when moved elsewhere).
Here are my Library settings as well:

At various points, I tried setting the monitored folder to M:\Music\MusicBee\Music\, but that did not seem to have an effect. Additionally, there were instances where the auto-organizer would move the files out of the folder specified in the primary template, but they would just get dumped in M:\Music\MusicBee\Music instead of in the Artist folder as specified. I wasn't sure what specific settings were causing this to happen though, and I was having trouble recreating it. Any thoughts?
EDITI've been doing more digging, and found something else. I wanted to see if I had the same issues with the auto-organizer if the files were on another drive, so I did the same thing with files on my C:\ drive, changing it so that files moved into MB from C:\ were kept on C:\. That worked fine, and surprisingly, exceptions on the M:\ drive started working too.

However, after changing it back so that files from the C:\ drive were moved to the M:\, the C:\ exceptions were still fine but the M:\ exceptions were not.

At first, my mind goes to maybe a permissions problem of some sorts, but if that were the case, then how is it able to revert back to the primary template?
EDIT AGAINI didn't notice this at first, but it's also applying the exceptions for the C:\ drive to files that are already stored on the M:\ drive.

I tinkered some more, and it looks like all my exceptions for the C:\ drive were being applied to everything in my library, even files that had never been on my C:\ drive.

So to recap: M:\ exceptions work when it's set up so that files on C:\ stay on C:\. When it's set so that files on C:\ are moved to M:\, then exceptions for M:\ do not work, and all exceptions on C:\ are applied to files that are being moved from C:\ to M:\ as well as files that were only ever on M:\. Is there something I am not understanding?