Don't know of who do adjust for surfacing (other than, perhaps some of the mail order places who deal in specialty project pieces and I'm not even sure of that for other than thin pieces which aren't normally priced by bd-ft anyway). As I noted previously, it's based on the raw stock size before any surfacing. Any place that will base the bd-ft value on surfaced thickness will adjust the price/bd-ft to reflect the original stock as they will certainly have that as the cost basis in buying the material.
And in case I misinterpreted your meaning above, actually, they calculate by thickness, just that in the case of 4/4 stock it's "1" so it numerically is the same. Buy some 6/4 stock and see if they "ignore" it then... :)
And for point three, just in case, the point was to a bd-ft to OP who I thought as he noted he was new to buying hardwoods might just not actually know...