I say go ahead and store the stuff in the boat, like you said, as long as its not too heavy. I would also pull it all out once home to let everything dry well. At least open the hatch cover.

Anything to make it easier to get out on the water quickly.

Yep, make sure that hatch cover is secure while driving. Make sure the stuff in the hatch isn't pushing the cover up. I can't think of any other reason for the warning.