Based on the below comparison of an EFI 5.9 to an MP 300 HP crate motor, I find it hard to believe that anything without a cam swap would see much difference regardless of the intake or exhaust side changes.
One variable though is that Holdener used an aftermarket EFI pcm, so it could be the stock tune causes some laziness.
I would speculate that a stock 5.9 compared to a basic LA 360 might rev better due to thinner piston rings, a roller cam, lighter rotating assembly and better (stock) flowing heads. But just a guess.