Just updating this. I went through my LBS and sent it to Treks warranty department, after advice on here and from Trek on Instagram (who were very helpful). They've refused the warranty as they say it was due to 'External Factors' but don't elaborate as to what they might be. They also note that I was over the 2-year paint warranty, and whilst this is technically true, it was by a couple of days and I had already contacted Trek to ask about the problem before then.
So all in all, a little disappointed but not sure what else I can do. I would have preferred if they would have told me what the 'External Factors' might have been so I can prevent them in the future – but these are bikes designed to be ridden so in some regard you would expect them to hold up to external factors. My LBS noted that they hadn't seen marks like these before, so could offer no guidance.
It will certainly give me some food for thought. I change bikes regularly and I'm not sure my next one will be a Trek. Perhaps someone else will find this useful as well if they are considering a purchase.
by BloodSexMagik