Your not being to picky, it's your money. The thin layer on the skylight is the inner layer. There should be a thicker outer layer.
The scratch and poor seam, I would ask the dealer to fix it. Even if they will only cover part of the costs I would get it fixed, otherwise you'll always notice it.
TV: 2013 F350, Lariat, 4x4, CC, LB, 6.7L Powerstroke
FW: 2013 Jayco Eagle Premier 361 REQS
Additions: Onan 5500W LP Generator, Surge Guard TS,
.......Roof Satellite Dish, Vent Covers, Bedroom Vent Fan,
.......Rear Reciever, 12V DC Outlets (6), 320W Solar & Controller,
.......4 Lifeline AGM Batteries (600 Ah @ 12V),
.......Stereo Upgraded, Interior Speaker Upgrade, Amp