With Dumbledore and Flitwick, we were never given an in-movie explanation.
Since we already saw Grindelwald change his appearance from Farrell to Depp (without polyjuice potion), it could easily be explained that ‘he just knows how to do that’ when he becomes Mikkelsen.
I don’t think a deepfake is necessary. Unless they bungle it.
And frankly, the Fantastic Beasts movies, so far, have seemed bungled.