With one repo you still have versions of this problem – have the flags been deployed as config to the flag system before the server build, has the server build removing usage rolled out fully by the time you remove the config. Using an RDBMS is an option, but makes scaling harder, you still need an audit trail, review processes, etc, so you eventually end up building a source control system on top of it (assuming you hit all the sharp corners and put time into solving them).
If you're feature flagging client code (i.e. somewhere you don't control rollouts, like mobile and web apps) that adds another layer of complexity.
While it's nice to have a simple system, having built one from scratch and used very mature feature flagging systems, my experience is that production systems hit almost all the edge cases quite quickly and flagging/experimentation systems are forced to evolve quite quickly to actually account for these issues.
Multi-repo or not isn't really an issue. My previous company had flag config in a separate repo, my current company has a monorepo, it doesn't really make a difference.