No, I am not really worried about the additional risk from the disc going .4" lower, I don't think it really makes a difference as I haven't bent one yet. Switching to a 300mm disc is easy if you are.
You seem to imply that I think this bike will be able to do everything better than a 990, which I do not. Obviously the focus of this lighter and smaller twin would not be to be a good 2-up with lots of luggage tourer. If that's what you want, then you already have the 990 available.
In practical application, speaking from my own experience and that of most owners of a F650GS twin, the single disc will work fine even with a 300mm disc, on a heavier bike.