I can’t tell if this is narrowly worded to only talk about copyright because you don’t know it was built from decompiled TTD, that source code is copyrightable, and TTD is a trademark. or, you do know, but feel the current IP rights regime is illegitimate. And I don’t want to insult you by quietly assuming the first, so figured I’d spell it out.
I’m usually sentimentally open to IP rights being overly constrictive in the current regime, but faced with a company that owns TTD™ saying “hey, instead of going full lawyer nastygram to avoid confusion, let’s work this out so people get your stuff when they download ours”…seems pretty nice. Like I can’t imagine Microsoft allowing alt-universe OpenWindows™ on the Windows Store.
I think the registered trademark is Transport Tycoon not TTD. The public may have called it TTD, but I'm not sure they used it in trade (IANAL, not legal advice). And I don't think the OpenTTD devs call it "Open Transport Tycoon Deluxe" anywhere. So the trademark case against the OpenTTD devs is likely pretty weak.
I personally think it is the copyright that is the most uncertain. Firstly, there are probably quite a few venues around the world where Atari might be able to take this up, and quite a diversity of precedent between them. Historically Atari litigated in the US - in 1981 they lost https://en.wikipedia.org/wiki/Atari_v._Amusement_World on a case someone infringed by copying their look and feel without copying any assets. Other precedents in that jurisdiction have found it's not infringing if similarities are inherent to the subject matter of the game: https://en.wikipedia.org/wiki/Data_East_USA,_Inc._v._Epyx,_I.... but similarity of art style is copyrightable: https://en.wikipedia.org/wiki/Tetris_Holding,_LLC_v._Xio_Int....