the .pcm file contains all of the games sound/music files.
the .rom file has had the .pcm data 'patched' out, if you check the .rom in hex you can see the data area is now filled with PCM in large sections of the rom file. Ive done much VC editing and my understanding of it would be with the way that Nintendos emulator works, and that an external .PCM file makes it somehow easier for the emulator to handle, possibly giving the emulator less decompression work or something i dont know.
I have previously succeeded in patching other roms to use these official .pcm files, for instance translated roms, but im yet to find anyone interested enough to look at the actual structure of .pcm or a method of 'repatching' the pcm back into the rom. I have only briefly discussed with people such as cowering.
A few other things of interest is that YES Nintendo do hacking on VC roms to fix typos/bugs/advertising rights and even to edit politically correctness of some games
Also for some roms that use special graphics chips they use a similar method as .pcm files and use external graphics files for the roms.
END SUGGESTION: I dont know of a way to merge the .pcm files back into the VC rom but your best bet is to use the super mario collection 'good dump' rom, hex search the PCM patched offsets in the VC rom and patched with the corresponding bytes from the 'good dump' rom. Ive done this previoulsy with some roms during my testing for rom injection, and yes sound and music worked perfectly
(oh, and be sure to remove headers off the good dump rom first)
(BTW this is my new ID, ive been around for a while)