I believe Alembic uses a 'grain filler' or leveler on top of the actual wood before adding other coats of whatever gets sprayed. Typically leveler has a slight wood tone to it, when I have refinished instruments using it.
This is a '76 Stingray I refinished a couple years back, that I first applied a grain filler to. It had originally been black, but the previous owner sanded it down some, so I went with a clear finish. The leveler imparted a pleasing vintage yellow tone to the wood, which is seen through the clear I applied.
You are correct that the stain could well be into the wood if this Elan was sanded down that far. To do a clear finish, all the stain would have to be removed, which means a lot of sanding. If it was refinished using a color, the refinisher would need to make sure that the stain was either removed or that it was capable of supporting a refin without lifting.