Short answer: yes. I always fit sights before finishing shaping of the buttstock.
I think you are asking about how to shape the stock so that sight alignment it almost instinctive. Good thing to consider and the cheekpiece definitely can affect this. However the answer can be different depending on the architecture of the gun. For example shotguns, where instinctive shooting and sight alignment is most important, do not have cheekrests or cheekpieces, etc. So this tells us that the comb line, drop at heel and comb, and width of the stock at the comb and mid-stock, determines most of the "automatic alignment".
On early guns, pre-percussion, the cheekpiece provides support for the jaw, not so much the cheek. It swells out the most at the part that your lower face rests on. On late percussion guns like Hawkens, the round cheekpiece supports more of the upper face as well.
But the amount of cast-off, height and width of the comb, etc are primary determinants of fit in my mind, and the cheekpiece is next.
Long winded, ain't I?
One way to assess fit is to smoothly mount the gun with eyes closed, then look at the sights. Hopefully if you do need to make adjustment, the rear sight will be to the right of the front so taking off wood will help line things up. Your face will leave oil residue on the stock and can give you an idea where to rasp a little. But in the end, on a rifle, there's usually some time for sight adjustment. Try to make any adjustments flow with the architecture.