Rather than "Favourite" how about trying to determine "Most Useful".
If ATC want to know when you be over point B while you over at point A, the means of determination will be the rate of change of your position over the surface. As you say, PBL, this will be slightly different from your rate of change of position REFERENCE the surface, but I can't really think of a useful application of that speed.
I suspect GPSes show the "Tangential" speed as that is the easiest one to determine, and the difference is, after all, pretty notional.