Have you actually looked at the property? The only "cottage" is the Garden Cottage, nice but it's on the beach. Accessible from anyone walking along that way. Too accessible to photographers from across the water. No way. As are both the Front and Back Lodges. I doubt they are in the stables or dog kennel or the cattle weighing house. After the car goes through the electric gate, you can't see which building it stops in front of.
Hinton Admiral is the Tapps-Gervis-Meyrick main home, where they do most of their charity from. Bodorgan was inherited from an aunt on his mothers side, I think. Just doubt the Meyrick's are actually there all that much. A suite of rooms in Boddargan Hall is my guess, where the young royals are living. It was asked once before "where do all the security stay?"
Well, a stately home that big has loads of room. And loads of staff. I seriously doubt the Duchess is cooking and washing his socks and scrubbing the sink while he's gone all day. There are plenty of other people on the estate to do such chores, including grocery shop. I seriously doubt Jean Louise Tapps-Gervis-Meyrick does her own grocery shopping, and she's not married to the Queen's grandson.
It IS the perfect solution, being as isolated and unknown as it is. Even people who research stately homes are unfamiliar with Bodorgan Hall. It's never been opened to the public, and few photos even exist. Someone at the palace looked into this thoroughly.
It is a nice little romantic story though, that they are renting the cottage from them, and picking up after themselves. I do wonder what one does with oneself knocking around a stately home (you don't own) all day? Bertie Wooster stories come to mind... Probably invite friends up to stay (secretly of course). Lawn croquette with the security? And occasionally telling the housekeeper, "Give me the list, I'll grocery shop!"
But hey, if you like the story, that's up to you. Personally, I'll eat my hat if it's true.