I have seen a number of variations but never where the labor charge was by the square regardless of the roof geometry. In most cases, we pay for steep, double steep, high, 2nd layer, ridge vent, chimney flash, skylights, etc.. In other words, in general, if we get paid a line item in the insurance scope, we pay the crew for doing it.
This seems to make sense to me. First, seems fair. Second, if the crew were only paid by the square, I'd have concerns about them taking shortcuts on items we didn't pay for. Unfortunately, the unpaid items that could be shorted are the areas where it may be most likely that leaks could occur down the road. Given we offer a 5 Year Workmanship Warranty, it would seem insane to try to save money now to only end up paying out much greater sums down the road.