I think the number 1 reason is going to be weight. A "standard" head with a black water holding tank will add extra weight to the trailer. You'll also have to carry more water, = more weight, for the flush. The Thetford in the TM is a recirculating head that uses the initial charge to do the flushing. The only extra liquid that is added is, well, not to be indelicate, your own. Also the rinsing of the "standard" black water tank is much more time consuming.
As far as the setup time goes, I think it will become a moot point once you get the hang of it. It sure sounds much more complicated than it really is, with a few runs under your belt. Takes the wife and me, at worst, 1/3 the time of the old popup. Initial leveling, disconnect from the TV, opening the TM, doing the interior, final leveling, awning, chairs, beer maybe 20 minutes if I'm realllllllllly slow.