Not sure if this is by design to have the structures partially damaged or what .. but I've ran into this particular castle a few times extremely damaged, seemingly missing whole walls ..

This just looks off and you end up with a lot of items on the ground (I see the contents of chests dumped out, stuff that should be on walls (like ladders), etc, lots of clutter on the ground.

Yes, this is intentional - it's a special block transformer called 'ruins'. It looks a bit better in the nightlies, and I do plan on improving it further in the future too.
This castle is currently the only build I have applied the transformer to, though.

Different castle .. even more broken .. I havn't see even a mostly whole one yet ..

(all images are different angles of the same)

Cool, as long as its something that you are keeping an eye on .. maybe I'm just overly picky about seeing a tonne of stuff strewn on the ground .. perhaps have the ruins code clean up loose entities on the ground soon after generation?

Yeah, the stuff on the ground is a side effect of not being able to turn off block drops on the fly. I mean, it's only logical - a wall crumbles, and the ladders fall to the ground - but I realize that in MC, dropped items feel kind of out of place. I'll try to address it in the future :)