Lots of great functions here, definitely improved my QoL. But I've got a couple suggestions regarding way shield/phase deployment interacts with the ship system.
First off, I'd suggest a functionality similar to how overloading handles it, meaning if I input right click while my system is active, only then would the shield reactivate after the system expires (otherwise remaining off). A lot of the time I'd prefer my defenses stay down after the system expires.
Secondly, and this feels like a bug, if your shields are active when activating a ship system with a duration (that does not disable shields), manually disabling them while the system is active still causes them to come back up after the system expires. Often this leaves you with the feeling that you're fighting against the controls.
Edit: unrelated, but "OffTextColor" is misspelled in the ini file and qolp_systemNotify.init() is causing a non-fatal exception