Looking to do some double sided milling and reading up on how to do it with good alignment. I think I have a handle on most of it but a little unsure on the origin point. My plan is to drill part way through for the location holes on the top (not drilling through the part and into the fixture). Then finish the top milling. Then mill the holes in the fixture piece, install the dowels and flip the part onto the dowels. I could take a break between the first side and milling the holes in the fixture without loosing accurate location of the pins which is a plus.

My main question is what to use for the origin. I know it needs to have the same x and y for both sides but Z may change. Lots of examples use the center of the part. Couldn't I use a corner or an end pin location? I think this should work but may not be as convenient. I am used to using a corner for the origin but maybe for this the center would work better. What are the trade offs?

Same plan should work for all materials but if it matters the final items will be steel.