So for the 3 people interested, I worked out that the function is implemented in TuneECU, and worked out the procedure by reading the service manual.
For anyone else with the same issue, TuneECU just triggers the crankshaft position adaption routine. I suspected it did as it let me run it, and if I cancelled it, the ECU disconnected me and I had to reconnect. I just didn't know the procedure, which needs the engine running (duh) and in my mind the thought of redlining the bike in neutral didn't sit well with me. However, from the service manual:
4. Hold the throttle fully open within 60 seconds of being prompted by the diagnostic tool. Do not close the throttle until instructed to do so by the diagnostic tool.
Note
• Upon holding the throttle open, the engine speed will increase and decrease in cycles at approximately one cycle per second. The cycles are repeated until the crankshaft position adaption is complete.
• Adaption is typically completed after the fourth cycle.
• You will be prompted to close the throttle when adaption has completed.
• The diagnostic tool will allow the test to operate with the throttle held open for a maximum of 10 seconds (approximately 10 cycles). If adaption is not completed in this time, the test will stop and you will be prompted to close the throttle and turn the ignition OFF. Note any on-screen messages and investigate the cause before attempting to restart the test.
5. Close the throttle when prompted by the diagnostic tool.
So I did it and yes, it revved up and down 4 times and stopped, and then Tune ECU told me to let go of the throttle and turn off the ignition for at least 120 seconds. On restart, code was cleared. Huzzah!