Each to their own here, I find the YM2149 absolutely horrific. Though, I was able to easily reproduced a YM2149 like sound using Logic Pro X's built in Retro Synth for a friend who does like the sound.
The whole Atari ST sound palette isn't something you can easily capture in something that isn't specifically made for the purpose. Check
this out.
I don't think you can you reasonably argue for the Atari ST sound being less distinct, unique and grungy than the Paula sound.
Back on topic, none of the Professional Music packages on the Atari wasted time with the Atari's internal audio hardware.
Back on topic? I think the above is highly relevant to the discussion. Whether the software is "professional" or not has nothing to do with the topic. As you said, the only reasonable use of these machines at this point is for whatever unique characteristics they had.
And no, the Atari ST isn't a "museum piece", people still use it for music.