The Atari is referred to as "being built like a tank" due to the shielding, but when did this stop being an issue? Did the FCC relax its requirements, or did RF interference simply become less of a problem now that people aren't as reliant on antennas anymore?
It never stopped to be an issue, only today there are better ways to solve it, mainly multilayer boards with internal ground and power planes and generally better understanding of EMC.
Apple basically found a way to game the system and ended up with a design that had fewer compromises and lower cost (on this front). I've heard several interviews on ANTIC The Atari 8-bit Podcast with various designers of the Atari computers who were very frustrated at being compelled to design their computers like a tank while Apple largely, in their view, just ignored the FCC and got away with it. Wikipedia has a more generous take on the situation, but even Wikipedia concedes that Apple was exploiting a loophole in the regulations.
Later, the FCC did relax its requirements, but by that point, Apple had established itself as the dominant player.