FWIW, I think best practice here is to hardcode all feature flags to off in the integration test suite, unless explicitly overwritten in a test. Otherwise you risk exactly these sorts of heisenbugs.
At a BigCo that’s probably going to require coordinating with an internal tools team, but worth getting it on their backlog. All tests should be as deterministic as possible, and this goes double for integration tests that can flake for reasons outside of the code.