I think I'm starting to get the hang of the manual tool. One thing I'm not sure is intentional or a bug is how the mask gets recalculated when changing things.
I noticed this when adding alignments for frames that were missing them, but had clear faces.
Basically, I use the bounding box tool to create a bounding box, and get it to look like it's correctly identifying the face.
Then I move to look at the mask view, and the mask that's generated seems to be based on the old/original location of the bounding box (where I first clicked to create it, before sizing/moving/tuning it).
To fix it, I have to go to the other box editor (location box? the green one), and make a change (e.g. slide it by a few pixels), at which point, if I go back into the mask view, it's correctly regenerated based on the landmarks.
Is this a bug? I think it might be, since redetecting landmarks by moving the bounding box should probably also regenerate the mask.