I think there are benefits to going either way, built-in, or aftermarket. I doubt the aftermarket units retain any bigger percentage of the original price than the article reports for the in-dash units. New car options in general, are a loser at resale time, most return much less than 50% of the original price....oh well....I am not about to do without A/C, and now, that I have NAV in my TCH, I won't do without it on my next car either.
I like my factory built-in unit for it's estetics, and the fact that I don't have dangling cords and the fear of theft whenever I park it outside of my garage. I agree, the aftermarket units offer some great features, specificaly the ability to take it with you and change cars, and a few more data points. (elevation, vehicle speed...)
Thanks for the link, interesting reading!