Yes full hitch and it is an OEM FJ Bridgestone tire in 265/70/17. Does seem that the smaller hitch would free up some space but no guarantee.
The best solution I've seen, outside of a full rear bumper, is Detours Offroad. They make custom hitch mounts that fold down or one that swings out...
I currently have an inflated 265/70/17 under mine but it does take a bit of manipulation to get it up there. I suppose I could fit a 275/70/18 (32.1") if deflated but it may rub on the rear sway bar b/c the 31.6" is VERY close already.
Your only suitable options w/ the factory 460 rails are either OEM or Inno. There are some Rhino options which include removal of the rails but they are expensive. I personally put a set of Prado rails on mine which are raised like the 470 and offer more crossbar options from Yakima/Thule but...
I think you are correct, there is no way that the GX460 wheels are et52. I always went with that assumption but after seeing many pics, including above, of 0 or near 0 offset wheels, i've come to the conclusion that the OEM wheels are indeed et25.
Can be as simple as lubricating the drive shaft. That clunk/knock typically occurs when coming to a stop and is very common across all the trucks w/ the 4.7L, Tundra, Sequoia, GX470, 100 series, etc.