This is an initial install afaik. Nothing is being "replaced', and even so, this is not an an usual issue for late model 7 diffs. Most are seeing tolerances such that significant bushing deflection is requiring to get the bolts through. I speak from experience, it seems you are speaking from speculation. "alignment" is not possible without force, because the hard rubber bushings need to deflect. This has been for many years actually if you go look at threads on blatchat going back ~10rs. There are various strategies in terms of order of operations, but it typically requires a lot force at some point in the process.