This topic had come up a couple of years ago. My understanding of the issue was that when riding an FJR with a top case, but no pillon, at "aggressive cruising" (aka triple digit) speeds, some riders experienced a shimmy / wobble / instability. They attributed it possibly to an aerodynamic condition caused by the void between the rider and the top case at those speeds, as the condition disappeared after replacing the void with body or baggage.
I don't have a top case, just passing along my recollection of the matter...
I believe it is also an extension of the Yamaha warning to not ride with the top case and panniers attached. IOW, legalize to free them from responsibility.
The wobble is not a "tank slapper" type (AFAIK) but more a high speed weave. When I used to run my Givi 42L at high speeds I got worse gas mileage. I believe that was caused by the vortices between rider and top case because those riding 2-up didn't suffer the same mileage loss. That would also explain the forces at work that could cause an issue with stability.
That being said, while riding on a private test track at speeds over 110 mph, my FJR was never unstable. I would think that loading or unloading the suspension on a road that rises and falls or sudden throttle changes might exacerbate the problem, as would any crosswind or headwind.
When traveling on extended trips I would put a Cortex tail bag between me and the top case (loaded with my tool kit, first aid kit, cleaning rags and sprays, etc.) and that eliminated the mileage loss and I never had any stability issues.
I think you should ride it and try it before assuming it is a widespread phenomenon. IF you have a problem, you now have a couple of suggestions as to "how" to ameliorate any issue.