OpenTTD has had entirely their own assets for 15 years.

The issue isn't the game assets. The division between assets and code is something id invented so they could open up their old game engines while still being able to sell[0] copies of the original DOOM. But that boundary is entirely a choice of the developer, and a consequence of separability of copyright - if you make something, you can break up the rights and hand them out in different ways. Legally speaking, the only thing that matters is if any part of OpenTTD is the same as any part of Transport Tycoon.

This part gets a little confusing in software, because we have a proud history of both cultural norms and actual caselaw allowing unauthorized reimplementation of other people's copyright-bearing APIs. Applying copyright to software basically created a mutant form of patent law that lasts forever, so the courts had to spend decades paring it back by defining boundaries between the two. Reimplementation precedent is part of that boundary.

But all of that precedent relies upon software compatibility - the argument being that if you lawfully use someone else's software library to write software, you are not surrendering ownership over your own program to your library vendor, and someone else with a compatible replacement is not infringing the original library.

Legal arguments relying on reimplementation work well when the APIs in question are minimally creative and there is a large amount of third-party software that used them. The closest example would be something like Ruffle, which reimplements a Flash Player runtime that was used for a countless number of games. OpenTTD exists to reimplement precisely one game, specifically to enable a bunch of unauthorized derivative works that would be facially illegal if they had been applied directly to the TTD source code. This wouldn't fly in court.

In court, OpenTTD would be judged based on substantial similarity between its code and Transport Tycoon's code. While copyright does not apply to game rules, and cloning a game is legal[1], I am not aware of any effort in OpenTTD to ensure their implementation of those rules is creatively distinct from Transport Tycoon's. In fact, OpenTTD was forked from a disassembly of the latter, which is highly likely[2] to produce substantial similarity.

tl;dr I'm genuinely surprised Atari didn't sue them off Steam!

[0] Translation for pedants: "have a monopoly on selling". In the creative biz, two people generally don't make money selling the same thing.

[1] Trade dress and trademark lawsuits notwithstanding - The Tetris Company has done an awful lot of litigation on that front.

[2] The standard way to avoid this is clean-room reverse engineering. It's not a legal requirement, of course, but it helps a lot.