Throttle is the vertical control, so that is expected.
4.1.0 is our latest stable ArduSub version, so that’s not out of date. Our Companion software is no longer being developed though - you may wish to try out BlueOS.
On the updating ArduSub front, if you have a slow internet connection to your Raspberry Pi you should still be able to download ArduSub firmware to your topside computer and do a direct upload of that to your autopilot board via the web interface of your Raspberry Pi software.