Real world anthropologists have the same issue- take away too much material and they have problems just the same.
You can easily extract a shell (or multiple shells) around the underlying skull and use the shell as a “minimum thickness”. Then when you’re sculpting and hit the shell, you now know how much further you have to go until you are to the skull underneath.
As Bezzo mentioned, his (and my) suggestion is just to get you closer to the desired effect as the current app doesn’t have that feature.