I get non-Lexus-specialized parts from my local Toyota dealers. If the part number is the same, it's the same part. I have two local dealers who are as cheap as anyone else in the country. I usually order online and pick it up. Brake lines, calipers, rotors, drive shafts, engine sensors, wheel bearings, HVAC actuators, etc, are more often than not shared between a GX and 4Runner of the same year. For a GX460, one would presume numerous engine parts are shared with a Tundra/Sequoia.
It appears the GX460 transmission can also be bought from a Toyota dealer:
Upgrade your vehicle's performance with our Remanufactured Automatic Transmission. Shop Genuine Toyota parts now!
autoparts.toyota.com
One of my preferred dealers has it for $3,200:
Upgrade your vehicle's performance with our Remanufactured Automatic Transmission. Shop Genuine Toyota parts now!
autoparts.bommaritotoyota.net