If you are thinking in terms of future value, then the salesman would be correct, as most who buy as an investment want the vehicle to be stock for the most part. And, while most small "improvements" such as electic ignition on older Mopars are usually over looked a sunroof is a major modification, and one that is not easy to return to original condition.
Additionally, many aftermarket sunroofs simply look to much like they were added.
Having said all that, it's your car and if you are making it for "you" and your enjoyment with no thought of resale value....than it's really up to you...do what makes you happy.
Personally, I wouldn't do it, but it's your call.
(I should state that I have the factory sunroof, and love it...but I knew I wanted the sunroof and so I purchased my Challenger with that in mind).