Dealer's make-ready scratched my tailgate when taking off another dealers nameplate (my dealer traded w/ another). These scratches (made w/ a screwdriver) were nearly all the way through the clearcoat. So I gave their body shop a chance to fix it. When I got it back, the area that they fixed was
smoooooth, with a GREAT shine, while the rest of the gate, after being blended, still had the original "orange-peel". I wouldn't let them touch the paint on the truck. When I went back to talk to the body shop manager, he told me that due to EPA regs regarding solvents, etc., that it was "impossible"

for them to duplicate the orange-peel. So now I am demanding a factory painted tailgate.
The BS manager told me straight out that color sanding or wet sanding WILL decrease the UV protection, as the clearcoat is about as thick as a matchbook cover.
So as far as options on your truck, if they sand it, they WILL reduce the UV protection on the roof, also may have the possibility of future peeling and/or fading. If they paint it, the part that they paint will most likely be much smoother than the rest of the truck.
If they could give me that smooth look on the whole truck w/o taking out the UV protection, I would do it in a micro-second, as it is alot nicer looking than the orange peel.
Good luck, I hope it works out for you. Le us know how it turns out.
__________________
Bryan

In memory of Chris- CaliforniaTitan
2004 Nissan Titan SE Kingcab
280 rwhp/ 333 max torque
Born on 03/31/2004--Came Home on 04/15/2004
Red Brawn--Graphite/Titanium
Big Tow, Utili-Trac Package, Rockford Fosgate w/ Power Captains Chairs, Rockford Fosgate Punch P550.2 Amp, 2-Rockford Fosgate Punch P110S4 10" Subs,
Tech12Volt Enclosure, TechTubes Polished SS Step Rails, OEM Fog Lights, OEM Bug Deflector, ARE LSII Hard Tonneau Cover, Black Stubby Antenna, Volant CAI,
AutoExtreme Throttle Body Spacer, Flo-Pro Dual Exhaust, Polished Aluminum Billet Grille, ChromeTailgate Accent, 18"X8.5" MB Offroad Gunner 6's,
265/70/18 Bridgestone Dueler A/T REVO's, Garmin nuvi 255W GPS, PRG Mini-Lift W/ 2½" Front Lift/ 1" Rear Blocks, LED's Front, Eagle Eyes LED Tails,
JDM 6000K HID Lows & Fogs, SilverStar Halogen High-beams, LED Third Brake Light, Red Billet Aluminum Oil Cap, Red Active Tuning Grounding Kit, Body Colored Front Spoiler,
2 Degree Timing Advance
, Clifford Matrix 50.5X Security/ Remote Start