This looks like some sort of abrasion process. Is there anything peculiar about the front notch of any of your Drives? The other thing I would check is the Click N Go for that drivewell to see that is securely mounted and allows no front, back or side movement with the Drive (up and down rocking is OK and should not cause any friction).
Just to be clear, is this happening in the forward part of the rear drivewell, correct? The reason I'm asking is because the PA 17 is the first that has a backward facing seat -- it would be good to eliminate this aspect from being a possible cause of the problem. Standard drivewells are reinforced differently at the front vs. the rear.
Finally, I wonder if a bubble or air pocket was trapped under that drivewell tongue. That would be very rare with the rotomolding process, but perhaps possible. To that end it would be good to know if this happened suddenly or progressively. There would be no way of knowing without further use to see if the wear continues, but the abrupt color change in your photo suggests a possible sudden collapse.
Your concern is understandable, but once you've dealt with Hobie for awhile, you will see it is not their style to try to cover up a defect or attempt to pin the blame on somebody. But when you're trying to get to the root of a unique issue like this, it's important to explore any any and all clues that may be related in an effort to solve the problem. Perhaps being in customer service for so long has made you a bit sensitive. Most here will assure you that Hobie takes good care of their customers. Since you appear to be the first person to have this problem and and the PA 17 has some unique capabilities, it's possible they may be related.

BTW I don't work for Hobie -- just sharing my opinion as a fellow forum member.