[Blue Streak 21]

I see what you mean. The tire is not centered in the wheel well, and the coil over is not centered in the upper A-arm opening. The coil over could hit the upper A-arm when driving over curbs or raised apex's. If you move the wheel to be centered in the wheel well, won't you bias the coil over farther toward the forward member of the upper A-arm? Or do UCA's fix both problems at the same time? I don't know how important this is. Maybe one of the Panoz Engr's could comment.
I used the same alignment method that you did. I positioned the upper control arm pivot to be in line with the longitundinal frame member. My positioning was similar to yours, in that I centered the bolts in the slots. The alignment was straight forward after I set the ride height and cross balanced the car. I'll have to look at how my car's suspension makes the wheel sit in the wheel well.