That reference means they recognize you can use any flue for venting as long as it meets the requirements for that appliance and the other code sections. Therefore, in order to vent a water heater or furnace into a fireplace flue, you would have to permanently block off the fireplace from the flue. The WH would then have to vent directly into the first flue tile. However, you still need at least 12" of flue to extend below the breech connection, which means the smoke chamber. You need access into the smoke chamber to inspect and clean out debris. The flue also would need to be inspected for suitability for that application (Level II). Since fireplace flues are generally much too large for heaters, it would require a listed liner regardless. If you still wanted to do this, you would have to remove the vented gas logs.
HTH,
Bob

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Keep the fire in the fireplace.