Well, not being a Lain collector (and at these YHJ starting prices unlikely to start, even though I know it's a major classic), here's my 500 yen.
The cel has got layers of tape across the top in two places. That makes it likely that the item has two layers: one, as you intuit, is the mouth layer and the other is the character either with closed mouth or (more likely) no mouth. So, yes, the sequence would likely have used a single A1 END partial layer of the character's face and three B layers for the different mouth shapes, and alternated them under the camera to lip-synch the dialog.
(Actually, as I understand, in anime, the seiyuu perform to the finished footage, matching their words to the animated lip motion. That's the opposite of the normal Disney procedure, where the voice actors cut their dialogue like a movie drama, then the animators work to match that.)
But one thing that bothers me is that the seller has put a sheet of paper under part of the cel, up to the cut number (16) but for no particular reason leaves the sequence numbers in darkness at the top right. Maybe all you'd see is a jumble of letters and numbers, and the seller thought that was messy. But as a collector I like to see that the sequence numbers are there and "look right." Actually, if you save the dealer's image and brighten it dramatically, you can see something up in the corner, but not distinctly enough to read.
The cut number is how most studios number the scenes: most TV episodes have around 280-320 cuts, and most studios just number these in one sequence from start to finish. So a cel from cut 16 would come from close to the beginning of whichever episode it appears in. Some studios are good about putting that on the top of cels (Pierrot especially) but most times it's put just on the cels on the top of the stack and left off the rest. This being a short set, it probably was put on the A1 END. It shows up a little to the left of the sequence numbers, inside the oblong registration hole on the right.
If the cut number makes sense (that is, you've found the image in the show and it does appear early in the episode), then that's a good sign.
Pity that the seller's description is so sparce. All I get from translations is that the douga doesn't come with it.