I haven't heard of module flag-driven development-- would love to hear more details.

We manage the cleanup issue by defining a "removal branch" that cleans up the feature flag at the same time the feature flag is introduced. This sticks around as a dormant pull request during the lifetime of the flag. It's not much overhead when this is done early. Cleanup does become painful when the code's not fresh in your mind.

Note that we do feature branches as well as feature flags-- trunk vs. branch based development is orthogonal to using feature flags.