I've been playing with the bags a bit more today. Here is the bags the way they sit right now. I have to tell you that this is pretty damn close. The main culprit that made it look so bad before was the angle of the camera, I was looking down at an angle while some of the other pictures were looking directly at the rear.
Here is my bike looking directly at the rear. My bags are 3.5" and they are so close to lining up that I don't see the big deal, the 3" bag would likely line up perfectly for someone looking to keep the stock fender.
If it wasn't perfect I think that it would be so close that nobody would notice unless you pointed it out. Mine is an 09 so I have a slightly longer fender and fascia than earlier models I think, which is maybe why mine lines up better??
PS...Skydoc....that's a hot bike. I dig Denim black..I wish it was available when I bought my 09.