Thought about swapping to a factory air setup for my '65 Dart since a guy in Bakersfield was selling a setup for $100 which I could get my next trip south, but glad I stayed with my after-market unit (dealer installed?).
Main advantage of the factory air is a more compact package in passenger compartment and integrated controls.
Disadvantages:
1. Firewall is different in factory AC cars. You must cut holes for AC tubes and I recall relocate the heater holes.
2. Need dash controls. Factory AC cars had a 5 button climate switch (think, at least my '69 Dart did). On the plus side, replacement 5 button switches are available (rare). I have never seen a new 4 button switch, but I was able to use a new 5 button swich in my Newport (non-factory air) by rewiring the pneumatic and electrical wiring (have drawing I can scan).
3. When you need to replace the heater core, it is much harder on a factory AC car. With an under-dash unit, you just move it out of the way to remove the simpler heater box.
4. The integrated controls are more complicated. An under-dash unit is "stand-alone". It has its own blower, so no need for a hot-water valve. You just don't run the main blower to insure no heating. The expansion valve is built into the under-dash units.
The under-dash unit in my Dart is fairly narrow and doesn't bump a passenger's knee. The unit in my Newport is much wider and though thin, I can't set it tight to the dash and still open the center tray, so it can bump a passenger. However, the bench seat is so wide, they still have plenty of room. Mainly an issue with a center passenger.
Either factory or under-dash, I would install a modern Sanyo compressor. They are small, light, and efficient. A few places sell SB brackets for it. I may make my own. My Dart had a Tecumseh compressor w/ same bolt pattern as my Newport's aluminum York (many Fords), but a massive cast iron body. Chrysler's RV2 is too heavy.