Nature of the beast
Well Quasi, you could align the belt to be right up against the rear flange, and it would STILL ride against the front flange. Been there. Yours, like mine, has been like that since it came out of the crate, which I think applies to most 998 RTs. You're just noticing it. In a perfect world, it would be great if we could get the belt to ride between the two flanges, but it isn't going to happen without moving the motor, and besides, the engineers didn't have a concern with front flange clearance, anyway. Otherwise, there would be a spec for that like there is for the triple.
The belt is so long that the side loads on it from that front flange appear to be insignificant. And you probably have no indication of excessive wear on the belt edge, either. Obviously it's your machine and you can try to re-engineer things under there if you want. But I stopped worrying about it 30,000 miles ago, because I'm NOT going to try to adjust engine mounting, and it hasn't caused a single operating issue. Vibration is a bigger concern to me and now that Doc has the new roller for our ribbed belts, I'm going to put that on and "forget about it".