The passenger would lean against the top box. It all depends on the type of top box and how the mounting placement is. Some top boxes sit too far back and require the passenger to lean too far back to reach that back rest. Some top boxes may sit too far forward and the seating position becomes cramped. I would guess that most mounting plates would allow you to move the top case slightly forward or back to suit your needs.
I currently use a Givi E46 top case and it sits at just the perfect spot for passenger comfort. She always wears her motorcycle jacket and the padding in the jacket rests up against the hinge of the top box. For trips less than a few hours it's perfect.
If we were to do an all day ride, I would just strap a thin blanket or something on there to keep the hinge of the top box from digging into her back and to make it more level across her back. For really long trips I'll also have two drysacks that sit on top of each side case. This gives her armrests as well and there's no chance of her falling off when she inevitably falls asleep. This are not the best pictures, but hopefully convey the idea.
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