@lyon00 have you tried 5.22 ?
i am using 5.22 and also have this problem on my surface 3 using built in bluetooth radio. I must re-pair the game pad after each boot. Have done a clean shutdown multiple times. There is a /userdata/system/bluetooth/bluetooth.tar file
Other observations in my case is that when pairing it some times says says it failed but it is actually paired and I can use the controller. Also when the controller goes to sleep it must be repaired after waking up the controller.