Ok I have a feeling the OP and the rest of us are thinking 2 completely different things. Is the base of the board covered in wax? If so it's in the base as well and they did iron it (or run it through the rollers), the base doesn't absorb all the wax, hence why we scrape it before riding.
If the shop charged you to just drip on drops of wax, post up the shop name here, and never go back to them again. A lot of shop employees don't know their shit, but I can't imagine a shop employee being that stupid.
That's what I was wondering when I asked if it's really just drops of wax. I can't beleive that's what he's really talking about.
However, I couldn't figure out what else he could mean, but I think you are right....he's thinking that since he can see the wax on the base that means it's not melted into the base