How did you transport the bike to the shop? Did you speak with the owner on the phone, or an employee? Next step may be to take the frame back to the shop and respectfully ask to speak to the owner and look at the workstands to see if the clamps they use match the indentations on the frame.
It is strange that the frame could be dented so badly without damaging the paint. There is some extremely remote possibility that a vacuum seal was somehow created inside the seat tube, and a pressure or temperature differential caused the tube to collapse... I can't think of anything else that could have caused this.
The dents may be able to be rolled out or pressed out with frame blocks. This would damage the paint. In Seattle I think Aaron Goss (Aaron's Bikes/Rat Rod Bikes) could do this or point you in the right direction.