Ultimately, if it's an AR-15-compatible upper (EDIT: and not an NFA lower), only the marking on the upper counts as far as caliber goes.
NFA has nothing to do with it, unless you're trying to put a barrel less than 16" on a non-NFA lower.
If you're insinuating that an NFA lower can't utilize a caliber other than what's on the form 1 or form 4, per NFA law the firearm must not be PERMANENTLY altered from the information provided on the form. You can SBR a lower and say "10.5-inch barrel" and "5.56x45/.223" as the caliber; as long as you have a 10.5" 5.56/.223 upper in your possession it doesn't matter what's on the rifle as long as it's not permanently altered so that it can't accept the original upper.