In 72-73 Jeep did use the TH400 behind the 304, however the case used was not the more common AMC case used from 74 to 79. If I remember correctly they used what was commonly called a 'Buick Nail-Head' case, which required a cast iron adapter ring for the engine to tranny, a spacer for the crank to flexplate, a unique flexplate and torque converter, and a unique adapter from the tranny to the Dana 20 transfer case. You would also need the transfer case shifter specific to the Commando, and the steering column and shift linkage for the tranny. The front and rear driveshafts are different lengths also.
This would be quite an involved conversion, unless you could find a donor automatic Commando with a rusted out body or blown engine. A donor 72-73 Wagoneer would get you quite a few parts, I'm just not sure how much of the linkages etc. would work. You could use the 74-79 TH400, as it would bolt to the block without the adapter, but the crank flange was changed between 73 and 74 and would require modification. Also, from 74 to 79 all the CJ-7s (from 76), Wagoneers and J-series trucks with automatics used the Borg-Warner Quadra-Trac full time transfer case. To use the D20 transfer case you would still need the adapter, either the factory Jeep one (which were usually broken), or one from Novak or Advance Adapters (not sure if they even still make them), and the correct output shaft for the TH400 as it is very different from the Quadra-Trac setup.
Don't get me wrong, it is do-able, it's more of a 'Is it really worth the expense?' kind of project. In my younger years I wouldn't have had too many qualms about it, but I had access to a lot of factory parts manuals and 35-40 years ago parts weren't as hard to find. I did have a 73 Commando 304 automatic years ago that I actually dropped a 360 auto with Quadra-Trac into. I even found a factory floor shifter and console from a 66-71 Jeepster Commando V6 Auto and fit that in. I really liked it and it drove great in the winter, too bad the body rusted out...
I hope this answers some of your questions.
