Had a body guy look at it today. He seems to think that the sealant under the clear is starting to crack. He didn't think it was the 2008's but he had to do about 30 hoods under warranty because of a similar issue that Subaru paid for.
I might try some heavier compound on an inconspicuous spot on the hood just to see what happens. I have some pretty major road rash on it anyways so it will need repaired sooner than later but the roof is in pretty good shape other than the scaling artifacts.