Practicalities of getting it up there aside (as I'm not a boaty and wouldn't have a clue), the first thing to check is the weight.......the weight of the tinny plus the weight of whatever rack/lifting system you are looking at. How does that compare to load rating of the roof set by Ford?
Also, do a google search for "roof rack failures" and have a look at the issues that surfaced maybe 6 months ago. Some manufacturers (the recent issues were with Rhino but I wouldn't be surprised to see of others were the same) reduced the load rating by about 1/3rd if you drove off road (so on anything other than smooth tarmac), and a few folks had fallen foul to this and had roof racks (or rather roof mountings) fail. Even if you're under the stated roof limit set by Ford, better to check with rack manufacturer if they stipulate different static/dynamic or on road / off road limits. I think the issue came down to the mounting system, and the upshot was this that use rivets were weaker and had the potential for the rivets to pull through the sheet metal of the roof.
A tinny & loader have got to be getting up there in terms of weight so better to check what the rack manufacturers state, and check the fitting instructions to see how they fix on.