One factor not mentioned is that large parts can deform small amounts with low levels of installation force. Between deformation from interference fits to other elastic movement, the tolerances required are dependent on the amount of force that can be used to assemble/service the item. Most tolerancing is described in terms of clearance fits for drop-in assembly techniques so the forces and deformations are assumed to be zero, but that is often not the case. For example, the reason for alternate tightening of fasteners on such things as engine heads and wheel lug-nuts is deformation.
Misalignment with a slot is typically a negligible error source if the misalignment is less than about 5 degrees due to the sine component being so small. As the mating part shifts the distance between the pins that is multiplied by the sine of the angle to result in side-to-side displacement. Since slots are typically not interference fits, the amount of side-to-side displacement is often on the same order of magnitude as the tightest slip fits. In any case, it is easy, and necessary, to do the calculations regarding all contributors.