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So I thought about this, first, there's how flat is the bed? Then, does it move, ( yes, it's heated, it moves, but likely not "that much" ) then how straight are your rails and ...
Then I thought "this is what software compensation is for". You should be repeatable, the loads don't change that much, ( and the measurements are the same coming from either direction? your Z axis acts nice? - Hmm, another potential can of worms, there's likely some "shimmy" with Z motion that affects all 3 dimensions. )
Oh, occurs to me, if the bed isn't flat, a 4mm sheet of AL. would be easy to scrape in. ( But that's the machinist cutting back in. )