Normally I update my MIAB through the same user account on the cli.
Last time I did it while I was logged in with another account (also sudo capable). After each update I manually change the backup port in management/backup.py. For some reason this wasn’t working anymore. I now see what the problem is. The latest update created the installation in /home/user2/mailinabox, where the previous installation was in /home/user1/mailinabox.
No, it is a result of using a different user for the install.
Sure, it is not the preferred behaviour — but the way to avoid such behaviour is to be consistent with the user doing the install/upgrade. Using the root user creates the installation files root/mailinabox, for example.