There's two issues:

1. OpenTTD is not a clean room rewrite. It started by disassembling the original game and manually converting to C++ on a piecemeal basis.

2. As the game was updated, sure lots of this code has been rewritten. Almost certainly the majority. But has all of it been legally rewritten? Ehh... much less clear.

This sort of process has generally been held to produce a derived work of whatever you're cloning, even if the final result no longer contains original code, hence why clean room reverse engineering even became a thing in the first place.

It's probably fuzzy enough at this stage that you could have a long expensive drawn out legal battle about it (and I suspect we'll see at least one for some other project in the coming years with the recent trend of "I had AI rewrite this GPL project to my MIT licensed clone"). Would OpenTTD win? Who knows. Could OpenTTD afford it? Certainly not.

Correct me if I'm wrong but wasn't BSD in a similar legal limbo for a while? In that case wouldn't there be precedent for such projects to be legally fine so long as they've existed long enough and been heavily modified?