Question one,
More to the point, there are 9 penetrations from the cockpit to the bottom of the hull in the PA14. One very large opening for the Mirage Drive, and 8 scupper holes. Two of those have screw in inserts. All of them are constructed such that they are "tubes" with attachment at both the cockpit floor in the area as well as at the opening in the bottom of the hull. They are molded in when the hull is molded so no water can get into the inside area of the boat between the upper and lower surfaces.
Question two.
You have a number of answers here that should help. I would add that for car or truck topping a front mounted receiver can accept a small boat winch that can make loading the PA14 up top very easy. Just turn a crank handle. I load up my PA14 with everything that I strap down inside the front and rear cockpits, and then pull it right up on top of the truck with a front mounted winch. My rack is made from stainless steel handicap shower bars, along with a very large foam pad area. I even put the little cart for towing the boat with the electric bike up there where it gets captured by the front of the Yak. I don;t have to lift the Yak at all. The strap system pulls it up and turns the nose down when the nose is up in the air. The straps go through the Mirage Drive hole so that pull point is at that hole. A secondary strap hooked to the front handle comes tight when the mirage hole is just below the roller and tips the front of the Yak down. The roller system has those two rails on the sides to keep the yak centered and it will not slip off on a side hill. If I had it to do over I think I would use the shower grab bars longitudinally to fit the hull. (about a foot apart)
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Hobie PA14 with a mod or two
Some random Modification Pictures