One piece of research actually showed that there was no correlation between the effects of foot orthoses on rearfoot motion and the change in symptoms – i.e. the amount orthoses changed alignment had no bearing on how much they improved pain.
Irrespective of all this evidence, what was clear was that orthoses worked. Patients found them comfortable and their symptoms generally improved. So we all believed we were successfully re-aligning skeletons, stopping pronation and reducing musculoskeletal symptoms in the process. Not until more and more work regarding forces/kinetics was produced did we have an answer to this apparent paradox. It became clear that orthoses significantly reduced the forces within injured tissues and this was much more closely linked to symptom reduction. It was also shown that they did not need to significantly alter kinematics (alignment) to reduce the kinetics (forces). This was contrary to all we thought we knew, and again demanded we change our mindset regarding orthoses and their effects away from the ‘motion’ paradigm and towards the ‘force’ paradigm.

In summary:
Orthoses may or may not change visual alignment (kinematics)
Kinematic changes (if any) may well be subject-specific
Orthoses will reduce forces within injured tissues or structures (and do not need to ‘re-align’ the skeleton to do this)
Custom made orthoses have not been shown to be better than prefabricated orthoses