There are actually cases this has happened in (e.g. re-releases using ScummVM under the hood; id basing products on community source ports, etc.), but it's not always that simple.

Chris Sawyer as creator for example is known to have particular opinions on this as I recall, and if you e.g. look over to film making there's also a hot debate over preserving original artistic intent and original creations over later remasters. OpenTTD is more than a maintenance upgrade, it's a continuation and a different game.

Honestly I think it's probably just OK what Atari has done here. Monetizing the original assets is well in their rights both legally and morally (especially considering e.g. royalities to Chris), OpenTTD remains available everywhere, they're monetarily supporting OpenTTS, gamers will find it.

Note that once a commercial company decides to ship a FOSS project, they also are much more invested in potentially controlling its direction to different ends. This setup keeps OpenTTD community-run and independent, free to make decisions independent of a commercial agenda. This also feels worth protecting.

Another example is Heroes III with VCMI and HotA and other similar things. Some are attempts to do a bug-for-bug "vanilla" recreation, others expand on it in defined ways, still others add new features "in the spirit" of the original.

When you get to the last, you can definitely see how the original creator/artists could disagree.