My 2006 Fusion has the dealer installed remote start and I love it. I went shopping for it 1st and when I went to the local aftermarket spot to get a price....1st thing he says is, "ugh....those Fords are a pain in the ass to install...". Needless to say, he's not getting MY car for the install! Price was comparable.
I am sure there have been $$ increases from my 2006 purchase but at that time, it was $300 + tax. You may want to double check that Viper system, the ole...."oops, I forgot to include the security interface module into the price quote." bait and switch can easily happen if he thinks he's got an easy mark to slide that one by.
My suggestion is simple, go with the Ford unit.