As near as I can figure it, the BFD does only a part of what Audyssey can do. The feedback destroyer can cut (or boost) specific frequency ranges. It does a good job as a parametric equalizer. Audyssey, though, corrects not only in the frequency domain but in the time domain. It corrects more room issues than simple deviations from flat frequency response.
In short, your BFD (and mine) don't seem to have much of a role to play anymore. That being said, if you like it, or want more freedom to experiment with EQ curves, or for that matter if you just really love using REW, I don't see the harm. I suppose you could even use both methods of equalization, taking your FR close to flat with the BFD and then letting Audyssey fine tune things. I would suggest that if you do this you treat the BFD as a part of the sub, and follow the general advice that once you leave all sub settings alone after running Audyssey.