I am not sure if this is exactly what the initial post is about, but I do a lot of re-arrangements at the start. In some games trying to be more historical and in some games totally in my own judgement.
I did try out tools for leaders, but it was a while ago and I can't remember if the tools could manage units commands (linking of leader to unit/stack). It would be nice to have sets of schemas for this. Not necessarily for all leaders, but for any leaders you care to use. You apply the schema to a saved game just at the start, and there you have it: your very own arrangement with 100+ mouse clicks less.
Some would perhaps say that this is an exploit as you probably only arrange (optimise) your own country leaders, but heck, I try to do that anyway while in the game. The only difference is that I would save tons of mouse clicks.