I'm sure I'm missing some context but what is Atari's role here exactly? Isn't OpenTTD an independent and fully legal project? What is Atari's basis for asking for a "compromise"?
Or is it just the case that the project maintainers got paid off?
Atari own all the IP and copyright.
While OpenTTD is open source, it's basis is really that the original game was reverse-engineered, originally using the original assets, and then rebuilt.
Also all the map data etc is owned by Atari, so you need to have a 'genuine' copy to access all the levels etc.
Atari probably threatened to take it down if there wouldn't be a compromise. So a compromise was worked out that wouldn't require a takedown.
These are not people ripping off TTD to make a buck. If you absolutely love the game so much that you spent 20 years modding it, you're going to have some respect for the original and the publisher and are probably glad they are interested again.
I get that it's not the same Atari as it was 30 years ago. But I liken it to you being a Beatles cover band and the estate of John Lennon reaches out to you, you're going to treat them with some sort of respect.