Thanks for finding this! While going through it, I found examples of similar problems going back to to 2018 on a Pi Zero.
After editing bt.helper, my SN 30 Pro seems to be working as intended (I think): after loading Emulation Station, the controller would pair itself when I powered it on. Tested with 2 reboots and 2 cold boots. I wonder why your device started crashing.
Not sure about the crashes on shutdown, but it was only once or twice across 10-15 reboots/shutdowns. Chalk it up to a buggy bt implementation, I suppose. Still no issues with the bt dongle, though. Received one of the new 8bitdo Pro 2 controllers yesterday. That's working well with the dongle as well.