Hello.
Yesterday I consulted tktk, a modder who's known to mess around with facegen data, and is teamed up with other modders who do so too, kapaer and himka, about this bug.
He told me Himka said "Phoneme and modifier applied-mechanism disappear in BSFaceGenAnimationData(internal data of TESV.exe) since Skyrim 1.9, I guess it's a deliberate change, but I don't know why reason."
A question for the devs, if you're reading this: why did you guys delete these entries? This has obviously caused really bad bugs, and it shows even in the CK, where neither phonemes nor modifiers work anymore in the face animation tab of NPCs, only expressions do. I think not only me, but a lot of other people would like to know if you guys plan on fixing this, because not only does it screw the mfg command people like to use to take screenshots, but it screws up lip-synching and causes NPCs to be unable to close their eyes when going to sleep and such, and that had never happened in previous games.