One of the things that you'll notice on the rules for regionals is that there is no rule stating that all the runners have to be from the same high school. It's just that your squad will be placed in the non-championship section if there not from the same HS. NBN also doesn't have a black-letter rule stating all relay participants must be from the same HS.
I suspect that this is because if the meet organizer states such a rule, the state associations will crack down on these de-facto teams. By not stating the rule explicitly, there's wiggle room. "Oh, it just so happens that everyone on our team is from XXXXX HS!"
The bottom line is that in my state I know of several rules that NXN violates. (Out of season organization by coach, amateur status violations, school teams competing outside of season, school teams competing in non-sanctioned events, school teams competing against private non-sanctioned schools, just to name a few.) Foot Locker has fewer violations, but still has issues.