The axle isn't bent and the calliper isn't mis-aligned. The hubs on the wife's FSR are fine as are the hubs on my tricross. In fact, the hubs we have issue with run smooth and seal as well as anything else of that price.
The issue is that you can set up the calliper to run without any contact and set the bars up straight. Then, drop the wheel out and turn the axle a quarter turn, refit and the calliper and stem are no longer aligned. I can see exactly what the problem is and it's a manufacturing thing. It can't be adjusted out. It looks like the axle doesn't share the axis with the hub shell.
I got no feedback from Specialized about this and the shop sad they'd never seen it before. They thought the lock nuts were not square (but it wasn't that). However, if it's what I think it is, I'd imagine the problem would be more wide spread.
Try it on your own Specialized hubs. Mark the axle with some tipex or such. Now try the axle at 12, 3, 6 and 9 o'clock and have a look at the rotor relative the the calliper. That relationship shouldn't change. These hubs are centred at 12 and 6, rub the outside pad at 3 and the inside pad at 9. (and yes, I do know how to fit a wheel properly in the drop out and no, there's no stray paint. I'd also be impressed if I could fit a wheel that badly with such consistency!)
I'm glad to hear from ac282 that it's not just me who's noticed this!
Cynic-al, not sure it's something that could be seen in pic. Certainly not any I'm capable of taking. I'm far better with a spoke key than a camera!