AFAIK it's about the lam top choice - exotic and/or dark woods like rosewood, bubinga etc. don't get any options except clear as a finish. Likewise, figured maple tops don't allow any opaque finishes.
This is just in the builder though - if you call them, they can double-check that you really want to put a tobacco burst that you won't be able to see on a rosewood top, or cover that $400 unique choice quilt maple top in goblin flake.
What wood/finish combo are you thinking of?