I nowadays use phenix.refine almost always in the first stages of the refinement and later usually move to refmac. Now I have two modest resolution structures which behave much better in phenix than in refmac.
B-factors on the other hand seem to be less restrained in phenix.
If I take the phenix refined coordinates, keep the aniso records from TLS and run some refmac cycles, my structure is better than average with regards to the clash scores (69 %). I do not know how valid refinement strategy this is. (Rfree-R = 5.4 %)