A CEL blocks out the ability to remote start? Or, is that a separate problem?
Good about the emissions testing. Under those circumstances, I would not worry too much about the CEL. Just get a good tune from a reputable source like LME, Unleashed, LET, etc and have them turn off the rear O2's.
The dealer can reset the codes, but the CEL will come back regardless of what they do short of replacing your aftermarket DP's with the factory ones. And you don't want that