Typically you don't go more than the aforementioned 3/4"-1" deep into the runner in either the head or either manifold.
Extrude Hone is good for dry flow (MP-EFI), not so much for wet flow (TBI/Carb) because it lacks the surface finish to keep partly atomized fuel in suspension. Same reason that you don't polish intake ports. I suppose that you could use a heavy grit and sand-blast after Extrude-Honing a wet flow intake. Sure seems like a bass-ackwards way of doing things, but it might have some merit.
