I personally would have an inch or so of covering on your bottom for a couple of reasons. To protect the bottom from accidental drops of rocks or other heavy objects, give your inverts and bottom dwellers something to rest or play in/on, easier removal or moving of encrusting coral and lastly if not least pure aesthetics.
More than likely you will have bare spots anyway but IMO you would still have the "natural" look
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 My aquarium is nothing but a smorgasbord for my cats.....
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