Hard shell covers painted to match the vehicle are standard on all 2006 US RAVs. The "Limited" version is a two piece cover (front and back) that snap/buckle together... allowing the outer cover to be LOCKED on. The base and sport models has a hard outer cover that's held on by an elastic/vinyl band (very tight fit).
What may be more important is the aspect ratio of the tires and the offset of the rims between the two 4.3 models. I would say that someone will have to take a chance and see whether it will fit or not.
Back when the 4.2 RAVs were first released, I really liked the hard spare tire cover. I took the chance and bought one from the dealer, and luckily the wheel/tire combo between the 4.1 and 4.2 were similar.