It's... complicated; they own Transport Tycoon Deluxe, its code, its assets and its IP.

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.