nothing wrong with neither, wondering if just buying a ready to bolt has more benefits.
Nope. Automatic cars are much easier on the driveline in general. The TH-400 is a specific build to the GTO if yours is still orginal. The trans had higher line pressure and the ability to shift manually - other mom/pop Pontiacs with TH-400 are not the same. If you simply wanted to purchase a rebuilt just because and wanted to set your original aside because you plan on doing figure-8 burnouts to show off at the Friday night Burger King get-together, then I can see it.
The TH-400 is pretty rugged for a street car, but if you are looking to put more HP into the engine and do a lot of weekend racing, then upgrade. If your TH-400 is operating fine, leave it alone. If you do have it rebuilt, make sure
your trans is rebuilt and not swapped out with some other rebuilt off-the-shelf TH-400. You will have serial numbers on it - write them down and take a few pics. Sorry to have to suggest this, but it seems there are many shady people.
Same with the rear end. Behind an automatic, they are fine. If you have a posi and add wide sticky tires and plan on doing those figure-8 burnouts and revving the engine up to 6K in neutral and dropping the stick into D in an attempt to lift the front tires and impress the Honda guys - then get a better rear end. If you have any leaks at the pinion, you can have a pinion seal installed. It wouldn't hurt to have new axle bearings/seals installed as they are more apt to go than the carrier bearings.
If you need peace of mind, add a towing/road service package to your car insurance or get AAA.