How are people supposed to understand the "nuance of the situation" when they aren't even sharing it? What is the problem to begin with? Why can't both projects continue to exist independently?

The bundling might feel necessary from Atari's side because OpenTTD would compete with Atari's re-release on platforms like Steam and GoG (unlike on OpenTTD's website, where you're already at the end of the funnel for OpenTTD specifically and therefore Atari doesn't feel like they're losing a sale).

The problem is copyright won't expire on the 1995 game until some time next century, while a French company that acquired Atari's name and copyrights 20 years ago is now asserting their exclusive rights over the IP.

OpenTTD started from the ip they now own, and it's possible Atari could try and prove that in court. I don't know if they would win, but why spend the legal fees here?