I think the reason feature flags are never removed is because the timeframe that a given feature-flag is top-of-mind is also when it's at its most useful. Later when it's calcified in place and the off-state may be broken/atrophied, no one is really thinking about it.
I'm also not convinced it's always a huge problem. I can imagine sometimes it is, but in most codebases I've worked on, it's more of an annoyance but not cracking the top 3 or 5 biggest problems we wanted to focus on.
IMHO the best solution is not something heavy handed like a policy that we only use run-time config for fixed timeframes, or a process where we regularly audit and prune old flags. It's simply to keep a record of the config changes over time so anyone interested can see the history, and a culture where every engineer is encouraged to take a little extra time to verify and remove dead stuff whenever it crosses their path .
