I’ve now confirmed QGC’s custom MAVLink command functionality, and written a post about how to set it up. You can set up a couple of commands for high and low servo PWM values, that you can then trigger with your joystick or with on-screen buttons 
The ArduSub firmware defines several unique joystick button functions that aren’t available in other firmwares. They could potentially be replicable with a lua script that monitors the MANUAL_CONTROL message button values (which we’re considering providing at some point), but for many functions it’s sufficient to just send direct MAVLink messages, which as mentioned can be done with QGC already