If I am reading this correctly, you have indentations. The key was that you identified this as occurring at seams. In the tire industry, we use the term "splices" - places where long, flat pieces overlap to form a hoop. It is common for the ply splices to be visible - and they are always there even when you can't see them.
I think the question now is how bad are they, and since you bought the tires used, is Pirelli going to do anything?
So, first, if you've described this correctly, the tires are merely .... oh, let's call it "appearance challenged" - and not structurally unsound. So you can use the tires without fear of failure, they just won't look as good as they could.
Second, the fact that they shipped the tires to inspect them, likely means there will be some sort of monetary compensation to you, the consumer. I suspect Pirelli is going to look for impact damage in the form of broken cords - and, again, if you have described this accurately, they will not find such and will replace the tires - I'm guessing free of charge, although, I'll bet the dealer may want to charge you for mounting and balancing.