I don’t know, but for really flexible/heterogeneous, peripheral domains it can make a huge difference and I don’t understand why.
For aquaporin in the ankyrin complex, we went from a messy 3.6Å consensus local refinement, to a clean 3.1Å local, and the only difference was using the outputs of volume alignment tools, no changes in the local refinement parameters. (@team maybe is this a bug? Should these two refinement strategies be equivalent?)