I think Toyota uses a shorter than standard receiver tube because of the tire clearance issue. The receiver insert (which may no longer be with your vehicle) that comes with your factory hitch also has a shorter tube than the aftermarket ones you normally buy.
You can either try finding a shorter receiver insert, or just take a hacksaw to the offending long one and make it shorter. Just shove it in without the spare, put the pin through the hole to locate it, and mark where it sticks out the front end of the tube. Any length beyond that isn't providing any support whatsoever, so you can cut if off with no ill effects.