Though it's no longer a clone, it literally was a clone when it first started (you were even supposed to supply your own totally legitimately acquired asset packs).
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.
CorsixTH requires Theme Hospital assets but we didn't clone or otherwise steal anything that we ship, we require you to supply the assets precisely because we aren't. I presume that's true of OpenTTD as well. In the United States copyright protection for games covers the art and text but not the rules and Oracle vs. Google established reimplentations being fair even when exposing the same api. Truely novel game rules can be protected by patents per Nintendo.
> you were even supposed to supply your own totally legitimately acquired asset packs
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.