They are not the same bloodlines though. The APHA was not started for crop out quarter horses. Yes they accepted them, but it was not formed for that reason. Tobiano is one of the main patterns. Tobiano has never been, nor will it ever be in AQHA horses.
It's also like saying that ApHC horses are exactly the same as AQHA or APHA horses. It is not true. Yes they share a lot of similar lines, but there are differences.