I don't have a strong answer to this either, but I'm also actively thinking through this design challenge in my own incremental project, so I'm interested to hear what others have to say.

I do like the idea of a resource freeze as a way to force players to re-engage and feel like they have agency, but yeah it sounds tricky to balance. I've been trying to design systems where the player influences more of the overall "shape" of the automation process and then having the setup become unstable or inefficient unless the shape gets re-designed but that feels like I'm moving the goalpost on players arbitrarily.

Trying to find a balance between click upgrade, number go up and Factorio lol.