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Not sure I see the harm here, or the error, for that matter.

Harm: the number counts up a little faster than it should, but it also counts down faster than it should when you check off those double-counted items.

Error: you claim it should be counting the union of those sets. That's one viewpoint. Here's another: an item that is flagged AND is overdue is a bigger issue than one that is flagged OR overdue. Why should 5 flagged items look the same as 5 flagged overdue items? If that dock badge number jumps I'm going to go investigate and hopefully do something about the situation. It would be most unhelpful of OmniFocus to suppress that indication that I'm falling behind!