Back then, the DMCA didn't exist, so it was perfectly legal to copy your own legally-purchased copy of a game to a different media.

As far as the sound goes, the Atari POKEY chip was better at sound effects, and the Commodore SID chip was better at music. The Commodore version of M.U.L.E. was ported from the Atari version. Since the music was also ported, the Atari version would naturally have better music. Had the Commodore music been re-written for the C-64, by a C-64 musician, it probably would have sounded much better.

As for me, I cut my teeth on the C-64, so I was used to two joysticks and the keyboard, which really wasn't all that bad. Four joysticks would have been nice, but not a deal breaker. In any case, the main thing that made M.U.L.E. great was the overall game play, not the graphics or sound.

Even with minor differences in game play, both versions are still really fun, and that's all that really matters.