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Yes, the magic rule for the MiM cap bottom plate spacing is known not to match the SkyWater rule set. The rule description in the SkyWater documentation is not only imprecise, but it's missing vital information about the rule implementation.

I just asked this of Skywater. The answer was metal3 connected to met3_bot_plate is considered part of the met_bottom_place and the rule to use is 1.2um.