When holes in the receiver don't match holes in standard mounts [base] or are off center, one can:
1) Drill and tap more holes [Swiss Cheese solution]
2) Weld over the holes and start over [Nuke option]
3) Make a custom mount [ all day long option]
4) Screw something down and lapp the rings [wreck the rings]
5) Modify the mount [ mod the cheapest part]
6) Don't get involved
I have been going for option 5)
To modify the mounts [Brownells calls them Weaver bases] I have modified a pair of V blocks.
Those hold the mounts by the edges.
I move over [make oblong] the hole with an end mill the same size as the hole.
I move over the countersink with an end mill the same size as the countersink.
I change the bottom radius height, radius size, or centering with an end mill [if there is one the right size] or boring head.
The alignment procedure starts by centering a reticle in a scope body. I used to put a scope in half rings and rotate, and then adjust the elevation and windage until the center of the cross hairs stayed on one spot on the target. Now I press the objective against a mirror and adjust until the two cross hair images over lap.
Then the screws to the mounts are put in loose. The scope is shimmed [with narrow stacks of tape] until the centered scope bore sights. Then wet epoxy is put between the mount and receiver. The scope is checked for bore sight again. When the epoxy hardens, the screws are removed, threads are cleaned, and the screws are tightened with loctite.
The scope should then be sighted in when centered and no ring lapping needed or desired.