Both could be perfectly calibrated and still give you different answers. (Although I'm happy to get my cyclecomputer to within 1% of a measured roll-down mile.)

The GPS takes a measurement every 100 ft. or so, and calculates the straight line distance between them. The (perfectly calibrated) computer measures how far the wheel travels. So any wobble adds distance to the computer, but not the GPS. On a larger scale, if you go around a corner, the GPS could be off by cos(45 degrees), worst case, while the computer correctly measures how far you rode around that corner.

It really only matters when you're trying to follow a cue sheet. And the important measure there is how far off either is from the measuring tool(s) of the person(s) who put the cue sheet together.