Mark,

In my experience with at least 40 SMs, the foot of the mainsail is normally about 6" +/- 1" from the boom when the sail head and the halyard are rigged to the swivel correctly. In all cases that I have seen where the foot is not 6" +/- 1" above the boom, it was because either the head or the halyard were rigged wrong. 

If your mainsail is rigged correctly at the head, the halyard is correctly attached to the swivel, and the sail foot is still 1-2" above the boom, I do not have enough knowledge to tell you that performance is impacted, but I do know that Amel did NOT cut the sail to where the foot was 1-2" above the boom. It could be OK...I simply do not know.

I hope that this helps you.

Best,