Since there seems to be so much confusion about this subject, I will try and clear this up. You can choose to believe a different reason if you want, but this is why they are drooped.
There is elasticity in the flaperon control system. If you lock the position of one flaperon, you can put pressure on the bottom of the other one and lift it approx. 1/8". This also happens in flight (remember basic flight physics- - - there is higher pressure on the bottom of the wing).
The droop is to compensate for this to make the flaperons align in trail while in flight.
The procedure in the PAP is just a check. It is not an adjustment procedure. All it means is that if the flaperons are rigged properly (each one drooped approx. 1/8"), if you put a clap on one so that it aligns with the wing tip, you should measure about a 1/4" of down deflection on the other flaperon.
It never says adjust one so that it is 1/4" down with the other at neutral. If you do this, the stick will not be centered in straight and level flight.
If the system is rigged properly, it technically wouldn't matter which one you clamped into alignment with the wing tip, the other should be displaced down 1/4".
That is the reason.