Update – I figured out part of what is happening to the temporary skills in the first point (1) above.
When the relevant skill is activated (e.g., Medusa Head), the temporary skill (Petrifying Visage) is automatically placed on the hotbar – on the *first* hotbar, amid all the seven bedrolls and five teleportation pyramids and other junk the game has added there.
To get that temporary skill onto an actually usable hotbar (e.g. hotbar #5), you have to cast the base skill, open the skillbook, and drag the temporary skill into place.
All of which would be fine as long as the temporary skill *stayed where you put it*.
For some reason every time a saved game is loaded, those skills are just deleted from the hotbar. So every single time they have to be put back into place.
All of this is so pointless. Just stop automatically changing everything around on me and moving all the buttons. Just let me decide what goes on the hotbar, and leave it where I put it.