The arris does not have to coincide with two surfaces of the wood. If you measure down say two inches (could be anything reasonable) from the top on the vertical face at each end, and then snap a line between those two points, you can use that line, instead of the crowned edge of the timber, to measure from. You would then layout the rafter seats by measuring off that line 2". In the middle, where it is crowned, you would still be measuring 2" off a straight line, which means you remove more material for the rafter seats there.