Are we talking GNSS only jobs, or GNSS + Total Stations or Total Station alone?
Scale factors can play a big role if you're constructing structures. Your stake out can be on the the money, but it doesn't mean that 100m on the ground = 100m on the grid.
I'd personally refrain from using any site calibrations, only using published Coordinate Systems. For the structures we're using Scale Factor Only 1.000000 setup on Access.
Site Calibration done wrong can look tip top on the screen and during set outs, but can me miles our, especially in elevation, from the local datum you're trying to tie into.