Because the Iron Boots and Hover Boots were Gear screen items rather that C-Button items in the original Ocarina of Time, Grezzo had to add in a special case to the new Inventory system to allow for these items to be obtained and used as button items, resulting in some unusual behavior.
It turns out that when you obtain both boots normally in Ocarina of Time 3d, the game will update the proper flag within the byte that stores what Tunics/Boots have been obtained, just like it does in the N64 version. The game will use the flags within this byte to determine whether or not you have the boots and if you do, it will write the item value of the boot to it's corresponding item slot whenever you open the Item Menu, load a scene, or watch a cutscene.
What this means is that you can RBA over the Iron/Hover Boots item slots, but only if the appropriate boots flag within the Tunic & Boots byte isn't set. After you receive the boots you cannot directly RBA over them as the boots flag will prevent the boots slot from becoming overwritten.
Bottle Dupe will allow you to place a bottle over a boots item slot after receiving the item, but the item will still be displayed as boots, and once game checks that the boots flag isn't set again it'll revert back the item.
If you RBA with Mask of Truth on II, you can modify the byte that records what Tunics or Boots you've obtained, allowing you to RBA / Bottle Dupe over the Iron & Hover Boots. Mask of Truth RBA will not disable the Iron or Hover Boots.