Wow, it sounds like Trek has discovered a huge loophole in their warranty. I'm sure most people would do what you're doing, to avoid a more costly option. I guess the warranty is always at their discretion, but this makes it even more expensive for you should they rule against you. That really sucks.
One of the 2 Specialized frames I mentioned above was repainted without the decals, and it looked better. It was also cheaper. You should consider that, because why would you want to display their logo when they've not honored their warranty?
Well, I really hope you get your bike back soon, and it's as good as it was. You seem to be handling this very well.
'02 Eddy Merckx Fuga, Selle An Atomica
'85 Eddy Merckx Professional, Selle An Atomica
'10 Soma Double Cross DC, Selle An Atomica
Slacker on wheels.