There are numerous, straightforward solutions to this. Twitter can require third party apps to show ads, for instance. Twitter can continue to copy functionality from third party apps and then squeeze them down. Or Twitter can worry about this once they are monetizing the bulk of their user base at 99% of the potential.
I think this is genuinely a challenge for Twitter to solve, but I suspect (hope!) internally they spend much more time worrying about getting more users, how to meaningfully innovate and how to make Twitter more essential for the majority of their "sometimes" users.