Don't set the scope to the gun , set the gun up to you and your position .
A proper position does not always mean the top to bottom centerline of the rifle is square to the ground . Look at all the rifles in hi power for a bunch of examples with the adjustable space man stocks , ie Tubb rifles .
The important thing is that the reticule and tracking are square though .
The idea is to make it easier for you to shoot the rifle well not mount the accessories, if you are comfortable in your position you will shoot better because you won't be inducing stress by making your position fit the gun instead of the gun fit you . There is always more than 1 single way of getting something done , use the methods that work for you .