3 VA per square foot is for load calculations. How does this break down into point to point wiring? Other than the minimum number of circuits, it doesn’t. You could theoretically put every recep on one breaker except those requiring dedicated circuits. In fact I’ve found some houses very, very close to this.
I agree with the neutrals argument but only in that current carrying conductors should be the same length. That’s not a Code requirement but an engineering one. Under your rules THHN or MC would not be allowable wire types. I guess all commercial installs are huge Code violations.
It’s a Code violation to share neutrals but that wouldn’t be happening here after removing one breaker. You have one breaker, and possibly 2 neutrals at least from the MDP. Knowing the hits are tied together who knows how the neutrals run.
Often this happens where you have multiple switches or where a light and receptacle run together and the lights are on one circuit and receptacles on another. Somebody feels they are probably all the same circuit and just gets two big wire nuts. If you are in a gang box and don’t pay very close attention when you take it apart or something falls out all you see is black and white wires and sometimes red. Usually the assumption is everything in one box belongs to the same circuit. It’s easier that way.