I haven't worked on the games from the past few years but at least on the older stuff, the flippers aren't really cpu controlled other than a relay turning them entirely off or on, so to turn off one set and allow the other set to work you'd have to have a couple relays the cpu was controlling.... the typical way they used to do it at least was the end of stroke switch has another switch next to it that triggers the upper flipper, or you have doubled up cabinet switches on the buttons.
So you could disable one or the other but you'd have to add a relay to do that. In this particular game the ball can likely enter the upper playfield very quickly so relying on the cpu enabling and disabling certain flippers at certain times doesn't seem very useful to me.
There's just no real reason to turn off the top flippers. Every other game that has a third flipper or four flippers always has them flipping when the bottom ones do so I'm not sure why anybody needs to change that...