Obviously having OpenTTD available for free on Steam would jeopardize Atari's paid rerelease of Transport Tycoon Deluxe, so I think this is a good compromise. Hopefully they rigged it up so the assets from Transport Tycoon Deluxe get picked up automatically by OpenTTD when you install the bundle. I also hope that Atari will be sharing some of the revenue from the bundle with the OpenTTD team as part of this arrangement. They've spent the last 20+ years adding nice quality of life features and keeping the game playable, and I think they deserve to be rewarded for that effort. Going back to stock TTD after playing OpenTTD feels like a massive downgrade, like going from vim to BSD vi.
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I have nothing to base this on other than "it makes sense", but it seems like there has to be some form of revenue sharing here. OpenTTD is the reason why atari can even think this rerelease would work. I'm not saying there wouldn't be interest, but that I don't think any of the suits at atari would think to do this without OpenTTD keeping the interest there.