You not only waste time with "Remove feature flag X" stories if all customers end up with the feature, you also slow down the response time of some categories of bugs, because you end up having to stop and check the combination of feature flags to reproduce a bug.
And if you end up with a feature that isn't popular except by one customer, not only are you now stuck supporting "Legacy feature Y", you're actually stuck supporting, "Optional legacy feature Y" which is worse.
Maybe I'm ranting about "misuse of feature flags", but I don't like to pontificate about how things ought to be, but how in my experience they actually are.