I wish I could tell you how much extra torque to add for misalignment or the like, but I can’t. I have never seen anything in the literature on this subject, either. Yet I’m convinced that this factor can seriously degrade the relationship between tension in the bolts and clamping force between joint members, especially in large joint , as one example. Warped or nonflat (e.g., wavy) joint members , incidentally, could create the same sort of problem.