Comment 1 for bug 2003198

Probably cert-manager and nginx-ingress-controller auto-apply feature is disabled because they are manually applied during bootstrap. We could enable auto-apply feature for these apps checking if it is not during bootstrap and other possible conditions (the framework already accounts for restore and upgrades).
platform-integ-apps has the auto-apply feature enabled.
Don't know about other apps, will assume they don't have it enabled.