Sorry, do not know the exact OD of those holes on mine. I used the Eddy recommended intake bolt kit 8579 as the bolts that held the previous intake on were a mix-n-match of hex, 12 point and allen head.
I did not have any issues with the bolts laying down flush. That might just be an optical illusion where the cast boss is bigger on one side but the actual machined landing is parallel to the head face. May be harder to see on the smaller photo below.. but when I zoom in on the full sized photo on my desktop the landings on mine look much like yours.
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