Even with the E52, it doesn't throw the ride or handling off. The thing is to use common sense. When you pack the scooter, put heavier items in the underseat trunk to preserve the low center of gravity and forward weight bias. Lighter stuff goes in the top box. 90% of the time, I don't carry much up top, but I use that space to stow my riding gear when I stop. When I tour, I pack as stated above, with the heavier stuff down low.
The only drawback to the trunk is loss of about 7 mph top speed due to wind drag. When I was doing testing last Spring to determine the effect of various accessories, I topped out at 115 mph without the top box, and 108 mph with it (stock windscreen). Also, remember, the Givi mounting system is slick. A twist of a key and a push on one button is all it takes to remove the trunk. About 3 seconds to remove or reinstall it. So if for some reason you don't want to carry it on a particular ride, it is no big deal to remove it. The mounting rack is actually quite small and streamlined - the scoot doesn't look at all bad with the trunk removed.