I seemed to have made a poor choice by putting my h2 on a 1.57 inch scalarworks optic riser as most magnifiers don't line up at that height. 

How big of an issue is it if they are not perfectly aligned? Will it be inaccurate or just great effect my eye box. 

I'm currently looking at the primary arms extended eye relief magnifier which sits at 1.64 inches. Does a 2mm difference in height effect anything drastically? Or am I doing my normal overthinking?

I bought a magnifier once.  What I don't like about them is the weight and fixed magnification.  I have since moved on to LPVOs.

I don't know for sure but I don't think that deviation is a problem.  There are adjustments on the magnifier to center the dot in the field of view but keep in mind you only make zero adjustments on the Red Dot itself and then adjust the magnifier to center the dot in your view through the magnifier. 

If set on it I would get it through Amazon (same price as PA) but 30 day no hassle refund policy in case it doesn't work out.