In this case, since they're switching back-and-forth constantly, the CG Baby Yoda limits itself to the puppet's capabilities a lot more closely (and the puppet is probably capable of much more subtle and varied movements than the Yoda puppets ever were). Even so, Hertzog's "cowards" remarks notwithstanding, I wouldn't be surprised if there were many shots of the puppet doing puppet-things where it was replaced with the CG version to smooth out motion, hide seams or shadows, or introduce more subtleties. They did it all the time with BB-8, for instance, even in shots using a "real" one.