No, they don't. They own the game data, and the original game engine. They don't own the reimplemented Open Source game engine.
OpenTTD did not have to do anything here. It sounds like they had a very positive interaction with Atari, in which Atari is providing them with some support and collaboration, and in exchange for that, OpenTTD agreed to formalize the requirement for "you need to own the original game data" by having people on game stores purchase the original game through them before getting OpenTTD through them.
That seems like a pretty reasonable approach. It should be held up as a good model for collaboration. But it shouldn't be treated as "they have every right to [demand a] cease and desist".
So it'd be pretty much impossible to claim the engine came about as a clean room implementation. And of course, even if maybe they could win a court case (honestly don't think they could) the mere threat of one would likely make openttd quit.
I don't have the impression that OpenTTD encouraged or sanctioned obtaining those assets illegitimately. They talked about how to extract them from the original game that you owned.
Back when OpenTTD first released, it was a decompile (?) of TTD that loaded the assets of the game itself. This was... legally dubious, since reverse engineering.
But over time they Ship of Theseus'd the game - all code rewritten from assembly to C/C++ (I don't know), open source asset packs, etc. It's still the same base game, same feel, etc but nothing of the original code or assets remain.
I don't know enough about IP law etc to judge whether Atari would have any leg to stand on in a court of law, but it would be Complicated to say the least.
