But OpenTTD itself isn't a clean-room implementation of the game, it's a branch off a decompilation of the original game.

If Atari was really out to copyright the project into oblivion, they're likely to succeed in a legal sense*.

Within the confines of the current laws and known history of the game, and being a fan of both works, I think this compromise is fair.

*NotALawyerClause