Bit late, but I recently found an acceptable method myself. It was suggested elsewhere to use the [SYR] Set Up Camp mod; you reform the caravan and take the ship as an item, then immediately have the caravan set up camp and drop the ship from inventory, build it and then load your people/animals who are already carrying everything into the ship. This works, but is a bit clunky and requires the above mod.

What I've found works is to have one person board and launch the ship empty, go to an adjacent world tile. Then reform the caravan at the defeated site like in vanilla and hoard all the stuff, doesn't matter if you're massively overweight. Once the caravan is on the world map, launch the ship back to that tile. Voila, you can now merge the caravans and still launch without having to load the ship via hauling. Obviously this requires at least two people, one for the ship and one to stay behind to form the caravan, but no extra mods necessary.

I found the way to actually insta load the ship, you can see it here: https://steamcommunity.com/workshop/filedetails/discussion/1845423808/6274121610012552001/

damn