Take a look at this:

https://youtu.be/sXJmAhpAjeI

I haven't tried to set the BFO in my uBitX, so I can't really vouch to this, but it makes sense and is easy to follow.  It appears that it would affect both RX and TX, except TX in CW mode since that bypasses the BFO and uses Clock 2 from the Raduino directly.  
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Mark,
KE6BB