I figured out a solution for this customization problem.
Just like we have to run a script to install/update MiaB, there should be another script to enable customizations after updates. Sure, you’ll have to run an additional command (or set of them), but it’s better than nothing. I haven’t gotten started on any of this yet, but I think it’s a good solution.
As you surely already guessed, you need to edit/customize the usr/local/lib/roundcubemail/config.inc.php file and apply your custom preferences right after every new MiaB upgrade (manually or by running a custom script).