Generally can I fit 650b wheels on a modern CX frame? I know this depends a lot on the model and the shape of the stays and fork, but on the average CX disc frame would it be possible to use 650b wheels with thicker tires, for a more comfortable offroad (gravel) experience?
Wheel size swaps in bicycles are generally not possible, but this particular  rim and tire size swap is possible with disc brake equipped bikes, if you have the lateral tire clearance.

700c rims are 622mm in diameter at the bead seat. 650b rims are 584mm. The difference in radius - what has to be made up by a bigger tire - is 19mm. Assuming tire width is approximately tire height, going from a 28mm tire to a 42mm tire makes up most of that difference (42mm-28mm=14mm).

As an aside, changing rim diameter without a change in tire size is not recommended. Frames are designed around a certain wheel size and fitting a smaller rim size wheel negatively effects steering geometry and crank-ground clearance. 

See this Sheldon Brown article.