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It seems like the power requirement for the USB dongle permanently overwrites the (lower) power requirement for the integrated Bluetooth module. As a result the Bluetooth module thinks it is not supplied with sufficient power and shuts down.
Apparently there is a workaround with certain old Bluetooth 2.0 dongles with similar power requirements to the internal Bluetooth module, 2 I had lying around, which didn't work - I now bought a third one from eBay that I hope will fix this. Can't use the Puck.js until then and can't afford the time to have my MacBook shipped for repairs.
In the thread they are even shipping around old Bluetooth dongles via post to fix this.
Wow, you can actually permanently brick on-board Bluetooth just by inserting a USB stick? that's crazy!