I just went through the same thing. I think the dealer may opt to install some systems because it can help him stay busy especially this time of year. Yes it may increase his profit but you should have already signed a purchase agreement, more money in his pocket vs. the factory.
I don't think there is a real quality issue having either place do it. I liked my dealer to install some of the electronics because I could give my input on installations. There shouldn't be any warranty issues. Since I've placed my order last December Raymarine came out with digital radomes and a much better C-series of plotters. I stayed with the E-series but changed to a digital radar. I may not have been able to do this if the factory installed or sent these things with the boat.
I had the factory install the dodger and cushions. I was able to look at a few factory dodgers and some custom ones. The factory did a good job with these so I went with them.
I haven't had many problems but I'm still early in the process. If you have a compotent dealer you shouldn't have any problems.