If I'm not mistaken, the superchips system actually downloads the true orignial map to the handset, so when you go back to standard it is the original factory map being put back. Superchips also resets the flash counter, so that there is no record of the changes it makes to the map.
The APR on the other hand loads up a generic map that is similar to the standard VAG map, but can be spotted if the ECU is sent back for inspection.
A friend of mine had his ECU sent back to Germany for inspection because they though he had a remap which caused a problem with the car. Luckily, it wasnt remapped, and he got sorted in the end, but it made me cautious.
So for me, superchips is a safer option while the car is under warranty. And the time taken to change programs isn't likely to be an issue for me, as I am sure once the remap is on it will stay on, unless the car is going to a stealer for service.
Feel free to correct me if I am wrong here.