Dave I'm curious about the bio-balls are you planning to keep them ? How much LR will you add ? Are you planning a reef or a FOWLR ? I don't remember from your first post what your plan was. Bio-balls provide no denitrification and your rock will be inefficient because of it.
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Your argument that diffusion through a rock is probably low and water will not really travel an appreciable distance, however, in terms of bacteria, it doesnt really have to.One of the things to consider is the formation of biofolms, and mixed layer biofilms. I think that the surface of all inert structures are coated with a two layer biofilm, the inner is comprised of anaerobes, breaking nitrates to N2 and O2 while the outer is aerobes. The aerobes protect the anaerobes and provide the nitrates. Such proximity of growth leads to a remarkably efficient system. This system is negated when we add a wet-dry type filter. In this case the anaerobes predominantly grow on the filter. Since the oxygen is extremely high at the filter they are unable to mask the anaerobes and we get a an uncoupled nitrogen cycle. The nitrates build up.
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live rock as bio filter