I guess there's a reason BMW went to a different setup on later models. It can be a slight compromise sometimes where you get a cross-over at a certain RPM. However I've never found it to be a problem on my GS. The balancing procedure is very simple, easier than on later models with a more complex setup (some kind of cable routing box).
I would be a lot more concerned about getting the jetting and accelerator pump squirts in sync. I've spent enough time fiddling with one FCR that I don't envy the man who has two. It should rip once dialed in though.