On my end, entering an amount in box 3 that is equal to that in box 2 but negative does cancel the amount (as you indicated) but there's a net picked up tax amount (in the example I have a net +$4k taxes is picked up when I enter $100k in box 2 and -$100k in box 3. It's strange since the 1099-MISC itself goes to 0 but not the net taxes. This is much like what I get when I enter $100k in box 2, nothing in box 3, and then -$100k as "Other reportable income" – taxes do NOT get all canceled out and a net +$4k of taxes is picked up. Also, entering something in box 3 when there wasn't any in the provided 1099-MISC may invite trouble – I prefer entering it as is and then canceling out through the route of entering an equal but negative amount in "Other reportable income" and explaining there, etc. Unfortunately, it's not working.
