I've seen this happen a couple of times, and I think Stoo on SB does this all the time.
Did I hear my name? I often raft off charter boats, but the Captains are all buddies of mine so it's as much for social reasons as anything. Generally, I prefer to have the wreck to myself, so I will wait until the other boats are gone before I dive.
Remember that in Tobermory, the law requires that your tie to a mooring at a wreck site, (or a charter boat) and that someone needs to be in the boat at all times. If you raft off a charter, and that charter boat leaves when you're down, your boat will be left at the moorning and on it's own. (Some sites are not in the Park... the Niagara, the Caves, Lady Dufferin, City of Cleveland etc.) but common sense would suggest that leaving a boat without a tender isn't terribly clever, although I have seen it done. You are also required to fly a dive flag (either will do) and register the boat at the park office (along with yourself) before diving there. I can't recall if there is a fee to register the boat, but I don't think so.
Many, many years ago, a friend of mine who owned the Bruce Isles at the time, returned from a trip to the Arabia to discover a little Zodiac tied off when he tried to dock. Apparently someone came out and asked the passengers on the Bruce Isles if they could tie off, but no one bothered to mention it to the Captain.
Needless to say, they scooted back out to the Arabia to find a couple of worried divers floating about at the mooring, wondering how long they were going to wait until they began the three mile swim back to Toby!
If anyone has any specific questions about Tobermory and the diving there, feel free to PM me. I have been diving there for 30+ years and live there for much of the summer. I'm not on here as often as I should be...