Nothing wrong with buying retail if you want manufacturer warranty. I hate when people compare on-line, unauthorized prices to authorized and fully manufacturer backed and warrantied retailers.
Anyways.....as you can see by now, prices vary from city to city. If you really want to see if their install price and time are in-line with your area, call up other dealers and ask them over the phone how long it would take to install a pair of comps, set of co-axials, a 4-channel amp and some subs in a prefab box, and ask them how much it would cost. If what the other dealers quote you is relatively close to what your shop is telling you, then I don't see anything wrong with it. If everyone tells you it's a 4hr job, and would only cost $300....then there may be a problem with your shop's quote.