They do appear to be a bit deeper in the body but I think it's a bit of an ilusion. a lot of the bodies out there have a lip on the bottom edge that attaches to the chassis out riggers. The CR body curves down past the chassis rails and the floor attaches it to the chassis. I think you might be right about the door line being a bit higher
Bernie has a homebush body on his and it looks super low when you are standing next to it but parked next to Phil's CR and they are about the same overall height.
There's tons of room in the engine bay with an LS1 because they are a very compact motor. Even compared to the 302 they are compact as the heads are more upright than splayed out. The manifold is also very low profile making it look smaller.
Cheers