Found out a little more information yesterday. So what happened was the shipping company used the loops to tie the boat down during shipping. They over tightened the straps and bent the crap out of the tie down loops.
My take after learning that, is it's not really a Tracker build or assembly issue. Maybe a slight design issue, but to J Franko's point, the design makes sense for cost. The dealer was directed by Tracker on the fix, so it's not the dealer doing something terrible either.
I actually called Tracker, they confirmed the cut holes would be the only way to access and replace the damaged tie down loops.
So I'm not judging/bashing the dealer, and I'm not judging/bashing Tracker. However, if my boat shows up with damaged loops, I will likely ask for a different boat. Though I did see the finished repairs and everything looked fine on that boat.
Thanks again for the all the input.