> how? if you have 100 feature flags in your system each with 3 potential states, which states do you run in your e2es?

You're going way out of your way to imagine problems where there are none. Feature flags are ephemeral and work as an ad-hoc release toggled at runtime. You create a feature flag, you commit the changes you need to commit behind the feature flag. Before switching the feature flag you run tests in preparation for the feature flag release, an finally you flip the flag. After that point, you either rollback the feature flag or you remove the feature flag.

This is not rocket science.