But then you won't catch the bug before it hits production :)
Yes it's kinda fractal of bad practices that have to align for this problem to occur, but that's the nature of tech debt.
One way I have seen this handled is to enforce restricting rollouts of a feature flag to 95% at most. That way turning a feature all the way on requires removing the flag from your codebase. It’s draconian, but honestly anything less than that leads to the situation you describe.
He’s not saying to alter any of the feature flags used for the test, but simply to record which were used during the test.
Simply logging doesn’t introduce any of the issues you are describing.
> I think best practice here is to hardcode all feature flags to off in the integration test suite
That's pretty clearly about forcing the flags to be off, i.e. altering them, and not about logging their values.
If you’re testing a new feature, you should have explicit tests for the enabled state (along with existing tests for the disabled state).
If you have bugs propagating up the stack from flags changing in low-level dependencies, the change to the dependency is probably not properly tested.
Alternatively, if the feature flag gates a change to the interface of the dependency, you should have explicit integration tests covering the systems on both sides of the change.