The TRD's upward wheel travel might be slightly different from the Trail Edition, but downward wheel travel should be relatively the same since they both use the same sway bar setup (excluding those models with KDSS of course). As for comparing the 4runner, of any trim, to a Rubicon or Raptor, that turns into an apple to oranges discussion IMHO. The Rubicon has two solid axles which seem to offer much more versatility in difficult terrain. The Raptor's pickup bed and suspension setup make it much more capable at desert running and hauling loads. The 4runner, by comparison, is excels at no one specific activity, but rather is fairly decent in a variety of applications...a jack of all trades SUV.
OP, congrats on the purchase!