Nope, center to center (technically along the optical axis). This is convention.
Airgaps and thicknesses are never measured edge-to-edge because lenses are almost always of different diameter. Doing that would lead to over-complication of the callouts.
The D25S is just an example of an aperture you could use. I make no claim to having rigorously analyze the setup.
it's hard to tell from the drawing but I think the aperture is offset to one side. You'd have to look at the solid model to know for sure. I thought I had checked it but it's been a while. Now you know why engineers insist on design reviews to check their work. You can try the D36S too. Or just use Waterhouse stops.
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