There was no issue with the alignment done to the car. The top of the tower or the cup is almost exactly where it sat before. I took a measurement from the side to the inner fender and then from the back to the rain tray. This allowed me to position it right. You could see where it sat against the inner fender so it was placed in that spot. The top edge was welded to the inner fender and then the pressed/hammered up from the bottom to get it to the right measurements. I am pretty sure its the same height and if not its really close. For me however, it was a not huge concern because I have coilovers that have a separate adjustment for just height so I could easily fix it there. This generation of VW does have camber adjustment and it is done by two bolts that attach the bottom of the strut/coilover to the wheel bearing housing and then caster is toe is done at the tie rod. Toe, camber and caster were all within spec after an alignment.
I did leave my coilover the same height as the other side and no issues so it must be pretty close to the right height if its not perfect.
Jason
Everlast 255EXT - Perfection
Everlast PowerPro 256 - UPS Demolished
Everlast MTS200s
12 Ton Shop Press
DeWalt Hand Tools/ChopSaw