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I haven't come up with a better way then what you are suggesting. I then keep a known list of clearance violations that are not cleared in the design and document these errors; this document stays with the design package. If there are any changes under the component these need to be studied very closely to make sure hidden errors don't creep in.
PADS need to be able to mount components on more layers than just top and bottom to get around this; I haven't had to do it that often to make it worth turning into a 'bright idea'.