There’s reasonable adjustability within the stock shock, so you’ve got some room for personalising the settings there, however many bikes will benefit from an aftermarket shock built to a rider’s specific needs. We don’t imagine the topbox/pannier recommendation is rear shock related though if that’s what you mean.

Hey Frank,
That’s an interesting question, I notice that Yamaha mention the possibility of the bike being overloaded with that luggage configuration, and they generally recommend only a low carrying weight maximum for most top boxes (it was 5kg when I had a genuine Yamaha set-up fitted to a FZ-06 years ago).
At the time I know I carried much more than that many times, however that was a personal risk I took, and I know other FZ-06 owners were also able to carry above the recommended max. At the time it could also have an effect on the front wheel coming up, which would probably be even more noticeable on the MT-09, with the torquey triple.

Just speculating here, but with both the panniers and topbox it’s possible there’s a similar consideration, especially if you’ve got a pillion on board, of exceeding the MT-09 Tracer’s recommended maximum weight or putting too much strain on the subframe.

On the Yamaha YShop site they note:

“WARNING: Hard Saddlebags and Top Case not recommended to be used together on MT-09 Tracer due to increased risk of overloading the motorcycle.”