On the original Atomic Edition CD, there was an audio track following the data containing a high-quality copy of the main Duke theme. Is there any particular reason a rip of this isn't included?

I'd like to know as well.
But for the mean time, you can download it from the 3D Realms FTP:
[url=ftp://ftp.3drealms.com/misc/grabbag.zip]ftp://ftp.3drealms.com/misc/grabbag.zip[/url]

Also, a lot of remixes both official and fan made are available here

I personally adore Chris Kline's version of Grabbag:
http://www.youtube.com/watch?v=g-y0MdPXslo
Low-quality MP3 here (go to Music, then down the page until you find Duke Nukem, then Download MP3):
http://www.vertexguy.com/
You can hear it in better quality in this Gametrailers vid:
http://www.gametrailers.com/player/36747.html

The Megadeath version of Grabbag is pretty cool too.

I like the E3 2001 trailer version myself alot.
Of course, nothing beats the original MIDI :P