That would be up to the individual technician, ultimately (and which way their boss is facing at the moment), but there are some very real liability concerns when working on any modified vehicle - whether that be hardware or software changes. I've not heard of any dealer willing to install an aftermarket tune, and, if they did, they'd need an HPTuners interface, LS1Edit or something similar. This won't work with a Tech II.
And, you'd need the new tune, which they would not be able to flash (unless it's the GMPP tune which is basically a waste of time).
Blue-ish 2006 2.4, Werks stage 1 turbo, Borla cat-back, DDM braces, Spec aluminum flywheel, Spec stage 2 clutch, Werks aluminum radiator, some gauges, RKSport hood, Morimoto FX-Rs, GReddy Profec, Norm's fenders
'07 GXP, Werks Big Wheel K04 and tune, Solo catless downpipe, TCE Wilwood 6 piston front brakes, 4-piston rears , stainless brake lines, slotted/drilled rotors, BC Racing BR coilovers, Performance Autowerks intercooler, DDMWorks CAI, charge pipes and braces, RPM rollbar