Harmony, as well as Animate Pro,
has a nice little masking feature.
Using an indicator color,
the cutter tool,
and the network view,
you can make mouth shapes
cut away from the head layer.
Using standard phonemes the auto lip-sync feature gives you
a head start on doing all your lip flap work.
It does need some finessing, but the mapping feature
makes it much easier and quicker to fix.