Did play too much with pad UI, but it seems to be it roughly suffers from same issues as base game’s hotbar - a management intensive UI, that refuses to respect organisational choices I made.
The only way I can see it becoming manageable (and I still believe that making hotbar a foundation of your UI design to be a bad choice to begin with) if for the game to:
1) remember where you assigned the skills when they disappear (like switching weapons, loosing access to spells) and reassigning them to those spaces if possible
2) notifying player that new spells are available for assignment and asking player to place them, rather than shoving them into first available slot.
No kidding, I abandoned my current run, as I have to do some UI management, and I would rather play something else, than do that.