Another solution that is very foreign to us in sweng, but is common practice in, say, aviation, is to have that fallback plan in a big thick book, and to have a light that says "Oh it's time to use the fallback plan", rather than require users to diagnose the issue and remember the fallback.
This was one of the key ideas in the design of critical systems*: Instead of automating the execution of a big branching plan, it is often preferable to automate just the detection of the next desirable state, then let the users execute the transition. This is because, if there is time, it allows all users to be fully cognizant of the inner state of the system and the reasons for that state, in case they need to take over.
The worst of both worlds is to automate yourself into a corner, gunk everything up, and then require the user to come in and do a back-breaking cleanup just to get to the point where they can diagnose this. My factorio experiences mirror this last case perfectly.
* "Joint Cognitive Systems" - Hollnagle&Woods