You will need six holes on each flange: three for the bolts, and three more to clearance frame rivets.
If you end up having to space down, then the rivets are no longer a problem. But shearing extended 8mm bolts off is. At the point of spacing down, I would consider punching out the captive nuts in the frame and tapping the framerails directly to a more robust 10mm. You can also weld non-JIS 10mm nuts to the bottom of the frame at that point which yields you both a nut and a spacer.
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