I'll say up front possibly this is a conflict with Story Progression but, when I remove autonomy and then switch to another family in my town, the previous one will have free will again, even if I go back and check and it says they do not. They are not where I leave them. I wall up a plumbot and power it down (for example) so it will stop consigning items in it's inventory. I switch to another house, and next thing I know the entire family I was on previously is out at the library, robot and all.

I check, and the autonomy is removed. When I focus on them, they stand around only interacting with sims who interact with them, but they got there somehow....

I'm trying to micro-manage that family and it's relatives in other homes, but this is my main issue.
I understand it's strange to want them to stand around motionless in their homes, but I do plan to switch back and forth several times in one sim day, and I hate having to then send them home from wherever they wandered off to. Anything I'm missing?

StoryProgression only controls pushes performed by its own system, it does not manage the meta-autonomy performed by the game itself without some sort of outside help.

That help being <a class="wiki_link" href="/GoHere">GoHere</a> in this suite. With it installed, the mod now checks your StoryProgression options for "Push: Allow At Night" and "Push: Allow During Day" options and stops all attempts by any part of the game from pushing those sims to visit lots.

It will not stop the sims from going into high autonomy if they appear on screen, however it should stop them from leaving their home-lot.

See if that works for you.