Not sure how to answer the first one can you give a bit more to that. I think I understand with Witchery as well as Ghost/Poltergeists but not known many mods like it besides the mod for 1.8.9 I think made by the Witchery's creator called: Intangible. But that mod is outdated and for 1.8.9 only also which obviously doesn't answer what your looking for. But I've not come across similar to what your looking for unfortunately unless other magic mods do similar or a morph mod but that's about my knowledge of options vaguely.
Fortifications... I can't think of one better than Ancient Warfare but a mod with similar things to what your looking for must exist. I just don't know of any unfortunately.
For village extensions, Village Box I found works pretty well. I know of another one but I can't remember the name of it right now.
The Ruins one is stumping me, are you after dungeon like small scale structures dotted around the world? At least that's my guess based on what I think I remember the mod being about. After checking it again, I think I know what you mean. But I can more so consider Dungeon mods I know of more so than this structure focused type of similarity to Ruins I think.
I think Dungeon Tactics covers similar to Chocolate Quest, since most others like Roguelike and Doomlike exist but don't do the same that your looking for I know (I miss Chocolate Quest ):
That's what I got for searching based on what you stated for categories as well as a few I've heard of as of right now (more so mods I've heard of but never used I'm pretty sure/shots in the dark of what I think is relevant to fit in with your requirements) or used before (Village Box).
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