I suggest referring to the June 2008 issue of Timber Framing for an article on snap line square rule.
Offsetting the line from a reference face keeps all the timbers (roughly) flush to that face, which is desired for outside walls or top of floors, for example. Using centerlines would center the timbers, and for timbers of varying thicknesses would require some mental gymnastics to offset them back to the flush face or snapping the line to some new datum other than centerline, hence back to "square" one. Unless you want all of your timbers of varying thickness centered.