I'm not talking about the previous apps portion. That would be handy, but like you say is not going to necessarily be what is intended. I'm talking about the point in time when CA Backup does its thing, and backs up your appdata. That way, if you lose your cache pool and are restoring from ground zero it gets restored with the backed up appdata set, which theoretically would match the containers you want to reinstall and get running, at least to a large extent.
Also, it would be handy if installing a container wouldn't immediately start it, but instead offer an option like VM's do, to set it up but not start. When I had to recreate my cache pool for real, the multi install put things back and started them in an order which created some errors and chaos, because of the way I have things set up with dependencies and scripted starts. Having everything restored but not started would be ideal.
I script some containers startup with logic that can't be handled with the built in binary auto start with delay. I need conditionals, some of which were handled by your deprecated auto start plugin, some of which I coded myself. Since auto start and delay are now part of the base, I just handle all the special case containers with scripts.