The problem is when you use feature flags for customer-bespoke reasons or to enable paid features. Then they’re always there and have to be tested in combinations which sucks.

Yeah, those things are called "user settings". If you need them, you need them, but pretending they are feature flags and trying to port the flags development methods into your settings will lead to nothing but tears.

It's so closely related and so often mistaken, feature flags and tenant features are two completely different things

Echoing sibling comments, feature flags are about managing the deployment of new product capabilities, and should always be short-lived. They're not an appropriate choice for any kind of long-lived capability, like anything that's per-customer, or paid vs. non-paid, or etc. Using feature flags for those kinds of things is a classic design mistake.