EDIT: Tried to redo the steps and can't get my dongle to work properly again... will work on that.
I'm not using Bean devices (I wish I could) but I had a similar issue with a program relying on BLE and since I found this topic when searching for a fix, I might as well post the workaround I found.
I'm using a GMYLE USB adapter with a BCM20702 chip inside (VendorId: 0x0A5C ProductId: 0x21E8) on an iMac 14,1 (it's actually a hackintosh) running Mac OS 10.12.2 (16C67).
With Bluetooth Explorer (Xcode Hardware IO / Additional Tools) I can still scan for BLE devices but I can no longer connect to them. I have the same problem on another application using CoreBluetooth whose delegate method didConnectPeripheral is never called. I assume that it's not an hardware issue since everything is working as expected when running on an El Capitan VM. The strange thing is that I can use my AirPods without a problem even though they are advertised as a BLE device.
For the moment I fixed this by replacing the IOBluetoothFamily.kext in S/L/E with the one I found in El Capitan (btw the guide you mentioned is not useful since dongles definitions are already in the plist file). Versions are 4.4.6f1 vs 5.0.2f4.
Probably the steps I followed (use them at your own risk), I may have rebooted 1-2 times. However you should preferably use a dedicated tool like Kext Wizard :
# kextunload IOBluetoothFamily.kext
# kextunload IOBluetoothHIDDriver.kext
# rm -Rf IOBluetoothFamily.kext
# rm -Rf IOBluetoothHIDDriver.kext
# cp -R location_of_the_kext IOBluetoothFamily.kext
# cp -R location_of_the_kext IOBluetoothHIDDriver.kext
# chown -R root:wheel IOBluetoothFamily.kext
# chown -R root:wheel IOBluetoothHIDDriver.kext
So it looks like Apple broke something in CoreBluetooth and/or the Broadcom driver in Sierra. Another strange thing is that official AirPort cards also use the same BCM chip. So Mac OS probably handles things differently depending on if it's an internal chip or an USB dongle.
I will try to investigate a bit more to understand what's not working. I will start by diff the packet logs I obtained on the two versions. I may upload later the kext.