If you're searching for the ultimate accuracy, forget about the reticle. First, you need a plumb bob. Align the vertical part of the reticle along the string (= parallel) and check if the cross tracks it perfectly when you dial the vertical turret. In this position a good scope should track the string, but sometimes it doesn't. So it does not matter if your cross is level or not, what is important is : when you dial the turret up or down, the cross must follow the string. Tilt the scope until it tracks correctly, nothing else matters. Once the scope is level (read : it perfectly tracks a vertical line) tighten your bubble level around the scope and that's it. Remember : a good scope is built so that the "vertical" line of the cross is really vertical when the cross tracks vertically but if there is a difference, you will have to choose between a tilted cross that tracks perfectly or a leveled cross that doesn't track perfectly, always discard the second option, but if it happens, only the center of the cross will be useful, all the mil dots around are canted and won't shoot dead center.
Keep in mind that a rail bubble level (attached to the gun) could give a less-than-perfect result because you cannot zero it, a scope bubble level can be zeroed as described above and is a better choice. Like if there were no horizontal turret because "in theory" the scope is aligned with the rail that is aligned with the barrel.
If the barrel and the cross are not on the same vertical line, it will not make you shoot two yards off center at 100 yards, I agree, but at a long range it can make a little difference. Same thing as the Coriolis effect, you don't take care of it until you shoot things that are very far away from you. There's a video on Youtube that shows what happens with a canted gun shooting at 600 yards.
