You can do all the Pixhawk setups using a USB cable to connect, instead of the 3DR Telemetry radios. The bit-rate is faster (115,000) and the USB powers the board for most things. (Not motor tests)
Compass Calibration is something of a pain with the USB attached because you have to keep turning/twisting backwards to avoid tying the cable around your MR, but the compass points write almost immediately so you get a bunch more points than via Telemetry Radio. (I've had 3000 plus points using USB.)
As I'm sure you know, updating firmware can ONLY be done via USB.