I made hardly any modifications. I did colour swap some pieces because I was eager to start building, so I will add more dark brown tiles, plants et cetera over the coming days and weeks when my next Bricklink orders arrive.
One thing I did change structurally was the pig's "sand pile" that extends into the bow. Using hinge bricks with jumpers and tiles seemed a bit fragile, so I grabbed some old Hinge Plate 1 x 2 with 2 Fingers (4276), combined it with its counterpart (2452) and enjoyed the small footprint and good stability of this part. (See last picture in my following gallery.)
The rooftop works brilliantly and is stable, thanks to the interlocking tiles - when I poke at the structure, the only thing moving is the Dark Tan wedge plate below from the original set, as it's only loosely attached in the original set. In fact, I like the cabin so much I would like to make another one for the other open deck (maybe adding some walls, similar to your construction that closes off the middle hull). Speaking of which - this is my favourite part of your modification, as it closes off the middle hull which is arguably on the doll house side of things in the original build.
Sure thing, here you go: