Tbh, I think the whole top box thing was never very well thought through in the first place. But it's just such a useful item, it's success has just swamped any issues. The bike's rear subframe is up to carrying the weight of a pillion after all, so why not weight in the box? I suspect it's more to do with the strength of the actual mounting points and bolts. There is, as far as I'm aware, no legal/construction and use guidance available so it's just down to what people want to make/fit.
There have been bikes with rear subframe issues, and recalls for replacement of the entire subframe have been issued in the past - there's a particular case in mind, but can't remember what bike it was, think it was a Suzuki. Also, you have to think about the strength of the lugs/locks that actually attach the box to the rack.
If you challenged Givi, if they gave you an answer at all, they'd probably say a passenger shouldn't lean their weight on the back pad - it's just for comfort if you did happen to go back against it!
But as I said, a little common sense goes a long way.