If I understand your question correctly, then yes, the GUI allows you to easily toggle through different repos. All repos you are connected to are shown when you right-click the tray icon.
Yes, if I use the regular GUI with tray icons then okay, but what about the web UI provided by a headless server?
You can start multiple server instances, one for each repository. Would this work?
Currently server and the UI is not multi-“tenant” for lack of a better word, it’s unlikely to change soon, but it’s not fundamentally impossible - just a huge change.
+1 I think this is the better option.