My opinion of boresighting tools is that they are worthless. It takes a certain amount of mechanical aptitude to ensure that the device is properly installed. If a person has trouble figuring out how to adjust a scope, why add the extra burden of making them learn to use a boresighting gizmo. Also the static bore axis is not always aligned with the direction the bullet is going when it leaves the muzzle.
For bolt guns it is easy, set the gun on a stable rest and adjust so the crosshairs line up with the same far-away object you see through the bore. (When moving the crosshairs to a fixed point, the adjustment labels will be backwards). Then take it to 25 yards and shoot. Adjust so you are an inch or so low. Then more out to 100 and shoot a group. If you were centered at 25 you will be at or above the top of the paper at 100. For the "getting on paper stage" you only need to take one shot before adjusting. But for actually centering on the POA, you need to shoot a group and take the average.
About mounting the scope 90 degrees to one side; it will not make any difference except that the labels on the turrets will be wrong. Up becomes left and right becomes up.