Everything except a ground tile (grass, wooden floor, chasm, etc.) is an entity, but technically speaking everything could be transformed to anything else, although it would get weird if a grass tile disappeared and run away. I had a bug once where AIs left their glyphs on the map and started moving as grass. Fun times. :)
The skills, technically everything you mentioned is doable, some of it might be available now like convert animal, there is a necro skill that turns someone to a friendly for a short time. I'll be writing an article about changing some configurations for the game this weekend and I could use this ability as an example to show how to add such things to the game.
Getting the mushroom from a dagger is a system limitation. Everything that goes into making an item can be partially restored when salvaging. I'll probably add some potions later on and turn that mushroom into poison.