At the same time, the open source community has absolutely no responsibility to make Atari profits here either. The outcome here is simply that open source is getting screwed over

It isn't kind hearted. Them trying to shut down openttd would lead to a gigantic clusterfuck that would hurt their sales. This is them trying to remove a direct competitor to them releasing a new game as much as possible, without generating community backlash - to maximise profits

These companies are not our friends

> open source is getting screwed over

It may have been "screwed over" if there was no access to the oss game. But you can still download the game from their website. They just do not want that these appear as competitors in steam/gog platforms, so they bundled the oss version. Both sides thought this was a reasonable resolution. Thus I don't see "screwing over" here.

And yet, they're also directly supporting the developers of OpenTTD via a donation and not giving them any legal harassment.

This is, at worst, a morally-neutral compromise that's far better than any worst-case scenario