Dan,
Point noted. This will only be an issue if your reference surface is part of the joinery (i.e. not in a housing which would be below the surface. I tend to house everything, ref. and non-ref., and doing reductions on ends of timbers also minimizes the effects of planing. There are still surfaces that would be affected in terms of tightness (like a 6x6 girt fully housed into a 8x8 post). I guess the amount that needs to be planed off must also be considered. My logic is that once the cutting is done, so is the majority of the handling. At this point all the dings and scratches can be planed out, the piece finished and bundled for the truck. I suppose one could plane, cut, then sand, etc. Also- I don't plane exterior (not visible) surfaces.
As is so often the case, there are many valid notions and methods. This is a great place to share and learn. Thanks!