Don't get the JBL. Get an aftermarket sound system. It will sound better. The JBL system is hard to upgrade later.
I think the TPMS can work in aftermarket wheels. You just take out the special valve stems and put them on the aftermarket rims. I think.
My truck is a TRD Sport. You can check my CarDomain to see what they look like. The Sport has a hood scoop, bigger wheels (17"), paint matched mirrors, grill, door handles, and bumpers. A Limited Slip Diff and a slightly stiffer suspension.
The OffRoad package will have a flat hood, chrome rear bumper and grill, and a locking diff.
The TRD OffRoad and the TRD Sport both have the same seats. They have a mesh-like material in the center of the seat. The base model seats have a print fabric and less bolstering on the sides.