I got to the Anna Marie build in your book. And since I have a similar project with the Anna Marie, it was an useful chapter for me. I was going to cut a hole in the layout to accomodate the ship without touching the hull, but your remark about the partially visible rudder and propeller that would leave a "nasty" join at the back of the ship ... I didn't though of that !
I find the Anna Marie is a perfect ship for Heavy lifts and project cargo, with its massive onboard cranes. But I would like to depic an open cargo bay, with a loaded locomotive inside. And since the floor of the cargo bay sits below see level, even with a waterline cut, I still need to make a hole in the layout.