To give players the option of playing with the original music. Possibly just personal preference.
Also, I can't be bothered looking up the filesize of these PWADs but size limitations may have had something to do with it. Keep in mind many of these were released in the mid-90s when CD burners and even widespread fast internet access were still not that common. It was alot easier to transport and use two 1Mb zipfiles on floppy disks than a single 2Mb file.