It's important to note that the Atari that exists today is nothing like the company that created the 2600 console in the seventies. That company has long since been dismantled and its parts absorbed into other companies. Depending on who you ask, Jack Tramiel did a lot of the initial damage that ruined the company. Infogrames acquired Atari Corp in 2004(?) and finished off the last vestiges of the company caring about its thriving fanbase. Infogrames stirred up a lot of trouble in the early 00's by sending cease and desist letters to homebrew programmers of the Atari 2600 even though at the time the console was nearing thirty years old and hadn't had an official game released for it in two decades.
Of course Infogrames doesn't care about your plans to build off of their game. It's "theirs", even though the RA2 community has done enough collective work to remake the game several times over.