Hello,
I am aware that JACK might have some issue when logging in and out of the system. That might be an issue for multi user systems unless you reboot instead of relog.
Having said that, studio-controls and autojack settings are per user, so you can leave studio-controls settings as default for the user that does not need JACK plugins. And you can setup a small login login script to send the “autojack” command so that JACK is forced to stop and restart, therefore solving your problem.
I hope this helps. If this is not enough, you can join matrix room for support, or leave a question in ask ubuntu. Support – Ubuntu Studio