I spoke with Thor today and the guy that answered the phone said he spent something like 20 years attaching roofs to RVs. He said that it's strictly cosmetic and as long as the rest of the membrane is glued down it won't be a problem. He advised me to keep an eye on it occasionally and do regular maintenance (wash it with mild soap and a brush and keep an eye on all of the Dicor adhesive to ensure there are no leaks) but otherwise don't worry about it.
I'm slightly paranoid about things like that but he really seemed to know his stuff and was in no hurry to get me off of the phone, which makes me feel better about it. We spent about 10 minutes just talking about the assembly process for TPO roofs which proved he knows his stuff.
At the end of the day, it's still under warranty and I now have it documented that I spoke with Thor about it, so I'm not losing any (more) sleep over it.
Were I you, I would definitely speak with the manufacturer, though, to at least get it documented that you made them aware of it.
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