I worked on the trailer a lot yesterday, including cutting down a 6’ Burning Bush and I was exhausted and went to park the Subaru in the garage, hitting the house with a hullavator!
Have you tried mounting the cradle to see if that alignment is toast? I took a slight ding on mine when I forgot the cradles were still up going into a parking garage a couple of years ago, but whatever I did was not much or fatal because they still work fine.
That said, mine were mounted with the brace around the square Thule bar, before they added the slot, so may be a bit more ding-tolerant than your design.