I think Gabel's got a handle on the difference between mill and square. In Mill, you can trust that the dimensions of the timbers will be close enough to their expected values that you can cut your mortises and housings to those dimensions. You don't have to reduce everything to the next smallest increment to account for significant variations in dimension. If you find an occasional deviation from what you expect, then make note of it and make the necessary adjustment on the mating timber (mapping). Regarding the reference face, if the outside face of the timber is too twisted or bowed to serve as the reference, then maybe that piece should be set aside as a "spare"?

And I always score. Leaves a cleaner saw cut, and there's none of the ambiguity of a fat pencil line. Just doesn't take much time if it's part of your routine. But the saw is accurate enough that we rarely need to pare the end grain back to the line. CB.