So I'm thinking don't sweat it at all man. I picked up a Capita Sierrascope and it has the same thing going on. The board is brand new and never been waxed. The base has "CAPiTA on it, and you can feel all the transitions from purple to black (base is purple and letters are black). I'm gonna wax it tonight, but I don't expect this will go away. I think its just part of the construction. I'm sorry I can't speak on anything technical, but I'm saying that my new board has the same thing that you're experiencing.
As for overheating the base, from all my research, I found that you want the base to warm up. This promotes wax uptake, as you need to "activate" the pores in your base. As for technicalities, I like the base to get warm to the touch on the top sheet. I'm feeling the topsheet as I move the iron. What I read and watched said do not let the top she get "hot" to touch, if so, stop immediately and cool down. Hope this helps.