As far as I understand (someone correct me if I'm wrong) games that are free / non-commercial and have zero revenue are not affected at all by this, they still don't have to pay anything regardless of the number of installs.
If the game is no longer being sold (and thus no longer commercial / having revenue), then I expect that even under those new rules Unity would also not charge the dev.
Only monetized games have to pay. If they stop selling the game, they shouldn't be affected anymore.
Also
Does the Unity Runtime Fee apply to pirated copies of games?
We are happy to work with any developer who has been the victim of piracy so that they are not unfairly hurt by unwanted installs. (source)
"Will games made with Unity phone-home to track installs?
We will refine how we collect install data over time with a goal of accurately understanding the number of times the Unity runtime is distributed. Any install data will be collected in accordance with our Privacy Policy and applicable privacy laws."
Sounds like they're gonna add tracking data to the game, so probably pirated installs won't count
“Will games made with Unity phone-home to track installs?
We will refine how we collect install data over time with a goal of accurately understanding the number of times the Unity runtime is distributed. Any install data will be collected in accordance with our Privacy Policy and applicable privacy laws.” They already do, and fuck you for asking.
It would be a shame if they were forced to follow through with this threat. Cult of the Lamb is a great game. I'd be curious to know if this changes their plans for their next big content update, which they'd tentatively moved to late 2023 back in August.