Found a fix. It looks like some sort of issue with how matlab is utilizing the /tmp directory. I don't fully understand what's happening, but as a hack, you can create an auxiliiary temp directory for MATLAB to use inside your home directory. I put it under the cache directory, like so:
Then matlab can be launched from command line with the environment variable for the TMPDIR exported as
TMPDIR=~/.cache/matlab-tmp matlab -desktop
Any changes to preferences made while using this surrogate temp directory should actually save and persist on your next session.
I'll probably rely on this temp directory from here on out, as I don't see an issue with using it. To launch matlab with this environment variable more easily, you can write up a shell script or add a desktop file like the following. Here's my ~/.local/share/applications/matlab.desktop, which tells Matlab to rely on the new tmp and purges its contents after you're done.
NOTE: Change <username> below to your username! This is only a placeholder, and leaving it unchanged may damage your system!
Comment=Scientific computing software
Exec=bash -c "export TMPDIR=/home/<username>/.cache/matlab-tmp; matlab -desktop; rm -r $TMPDIR/*"