I don't really recognise the problem that is being described. In my experience, recording distance cycled by GPS is phenomenally accurate.
My evidence: as a matter of course I record with two independent devices, both Garmin Edges, but different models. Over 100 miles they always measure within a tenth of a mile of each other, and the distance is equally close to that predicted using my standard route planning technique. I see this consistency repeated time after time. It may be worth noting that this is with autopause set completely off.
I've often started a ride by going straight up the A38 past Tewkesbury Abbey. Assuming I don't deviate from the most obvious route, 10 miles invariably clicks up as I pass the entrance gate, precisely as predicted by RideWithGPS, BikeHike, Plotaroute and no doubt others. Theoretically it's possible that everything is wrong by exactly the same amount...