Sorry, different forum
Short answer:
When I have had scooters with top-boxes I put as little weight in them as possible, its much better to have the weight between the wheels.
Long answer
a.
basic problems
The air closing behind you as you move will come mostly from one side and then from the other. at certain speeds this changing of sides becomes "astable" - the left airflow builds until it triggers right flow and vice versa it starts to feed off itself and oscilates, forming a kind of resonance where the forces get stronger and stronger until they start moving the bike, the bike wobbles, you correct it and add to the forces.
When this happens depends on speed, the bike, but it also depends on other stuff like size of rider, is a screen fitted? panniers? etc.
You can also get problems with fairings and luggage causing lift. Lift doesn't always act upwards, it can act sideways too. This can cause similar problems but also think about a bike in a turn. It is leant over and the low side is in aerodynamic "shadow". The bike may lift sideways and outwards at the same time
Or, the box might just just be a bloody big barn door in a crosswind
A top box can bugger up aerodynamics but it can also improve it (giving better mpg).
When the air closes behind you a top box can give it a neat place to join back up and the air flow treats you and the top box as one object instead with a theoretical bubble of air filling the gap and travelling with the bike. Alternatively it just pulls in behind you and smashes into the box as though it's an air brake. In reality you would expect a bit of both to go on but motorcycles have notoriously crap aerodynamics.
Either way, as the air fills in behind you it won't be absolutely perfect, it will swirl making spirals called vortices. It won't be perfectly aligned either because it wasn't still to begin with and you probably weren't travelling straight into the wind but at some angle to it. That is why the flow isn't perfectly balanced from each side
Your top box then acts to catch these forces, either by being hit by the airflow or as an aerodynamic element if its read about the bubble theory. The flow can also flicker between flowing round the bubble and cutting in sharply which causes the forces push on different areas of the bike and upset it (refered to as a shift in the centre of pressure)
b. If you want to design a top box commercially you have a problem, you have no idea what it is going to be stuck onto. Even if it is for a specific model range the dynamics change according to the size of the rider/2 up/ does it have panniers or a screen etc . That is why different riders will say that there top box has no effect, causes instability at this speed or that speed and so on. They can all be right, small changes can alter things a lot.
c.
Manufacterers problem No2.The box has to work up to a sensible speed. If you demand that it works at 70mph then you have to design it to for more than twice that.
Why?
Because 70 is the road speed, the airspeed might be much more because of wind - a 40 mph wind gives an airspeed of 70 + 40 = 110 mph. But the airflow is also jumping around all over the place because it has gone around you, your bike, oncoming traffic etc so its gusting; sometimes less than 110 sometimes more and a sudden gust from 0 to 110 can be more damaging than a constant high speed because it is a hammer blow so you need to have a margin for error to cover the extremes.
d.
weight Somebody once complained that there top box bit the dust and it was hardly carrying anything more than a pair of underpants. I bit my tongue but really wanted to point that it wasn't the undrpants that did the damage it was the half ton of camping gear six months ago that stressed it over every bump. It isn't just the load but how long it is applied for and how many flex cycles it goes through.
