Normal carbonation is around 2 volumes, right? (give or take). In a 22 oz bottle, that's 44 oz of CO2, (at STP, but stop splitting my hairs ). The equalization with 1 or 2 ounces of headspace is minimal.
Edit, in a 12 oz bottle, it's 24 oz CO2...assuming 1 oz headspace, that's 4% unfilled....assuming your beer equalizes with the headspace, you lose, what, at most 8%? (I'm going off of me carbonating beer at around 12 psi, which is about 0.8 atm, and since PV=nRT, PV is inversely proportional, so pressure doubles, volume halves, half the volume means you fit twice as much, so at a rough estimate double the % unfilled).
You really wanna be safe, I guess overcarb your beer by 4-8%?