When I use snaplines I relate the lines to what would be the reference face in edge square rule. before placing level lines on the ends of the timbers, I will split the difference in the twist or bow or whatever the timber is doing. In this way the surfaces will generally meet as well as they can. Surfaces that come out looking bad will be adjusted during fitting.
If you're dealing with wood, then you will always be using a bit of scribe technique to make it pretty.
