Firstly from an aesthetic point of view they're hideous, you'll end up having to buy a plastic piece of crap to hold it in and aftermarket stereos are just not great, it won't be flush to the rest of the dash.
Secondly depending on your car a bunch of stuff that used to work with your car (forward/reverse sensors) might not show up any more.
Thirdly stalk adaptors costs a fortune.
You really want a car that has got that experience sorted and after driving a modern VW, I'd say a VW or Audi is probably the way to go. They'll have Carplay/Auto/Mirror and that's what you want. The experience of an aftermarket stereo is just not great.
But many newer cars have totally custom, integrated audio systems and retrofitting is either extremely expensive or impossible.
In addition, to my knowledge older Volkswagen AG vehicles are ripe for replacing the infotainment with a newer, carplay enabled system, but on newer models it seems that it is rather locked down and not as easy a solution as you suggest.
On the flipside, some manufacturers impose limitations on what you can do when driving, which is annoying, so after market might get around some of that?
My last car, the "stereo" was just a control board with a screen and some buttons. The head-unit was actually under the seat. The space directly behind the stereo controller was air ducts and a center speaker.