No idea why this took so long to figure out, I blame society.
So apparently, swapping out the VS screen music does work, but you need to use simple vs screen in order to hear it (the second checkbox in the startup config)
The reason is pretty clear, usually the game loads a video file as the background, dat_m_vs.d
After a small suggestion from Sashi I tried renaming this file to .mpeg and surprisingly, the video loaded! Turns out you can take pretty much any video file you have a proper codec for and rename it to replace this file. I may be able to dynamically remux this video with the music of your choice and have that function in my music tool.
Proof of concept
http://www.youtube.com/watch?v=BDpyDUPPoxkNote that the replacement video was not of the same kind but still worked
I am also considering adding a function to dynamically modify the stage labels in game with track names when you use my application to deploy music packs, but I need a good font for this and I'm hoping someone with experience in design/typography can help me.