I discussed the 2-in window flange design with Steve. He had a couple of suggested changes. I'm adding them here for reference as I update the drawings.
He says the angling of the optic into the main flange is fine, 8" 40m flanges have this design.
Many of the finishing and tolerance parameters don't matter so much. Over toleranced parts will cost more. The only place where this might need to be careful is in the spec of the oring grove where vacuum is actually being held back, the 16 Ra in the drawing is fine.
Marco rubber and plastics have a good summary page for best practice design parameters, see: O-Ring Groove Design Directory.