Yeah, I was on the same page as you. Nevertheless, if a guy has been playing with the same people in the same spot in the order for a 3+ years... I think you would be deflating or inflating his projected runs and RBIs (because of his spot in the order and those batting around him) even though in this case you should probably do nothing. I believe most projection systems use around 3-5 years of data so the only way to validate what you're doing is compare against past line-ups and batting order positions during the years used for projection, which obviously gets too crazy.
UNLESS, projection systems like ZiPS / Steamer completely ignore past data for RBI and runs when projecting, but I doubt it.