Is the sound just worse on 7800 games, or does it affect 2600 compatibility?

I misspoke. The 7800's sound hardware is worse than the 5200's (which is the same as the Atari 8-bit), but is the same as the 2600. Still, having audio hardware (or, really, anything else) decrease in quality from the previous generation is not a virtue for the console or Atari.