A lot of GPSs measure long, eg if you ride 100 miles they might tell you it was 102 miles. You're riding in a fairly straight line most of the time, but GPS has a lot of jitter. Plus, depending how you carry your phone (how much view of the sky does it have?) and how much tree cover, there's more noise. Anyway it's only 2.5 % difference, so I wouldn't sweat it all that much. (But maybe check the wheel size in your non-GPS bike computer.)

Otherwise all your assumptions are correct.