The source is tcrf.net, a site that compiles beta elements and unused stuff, as well as comparing regional differences and other stuff.
Because I like wikis, I went to explore what they said about SSB3DS. Besides the same discoveries found here (ROM dumps and all that).
I found this:
Version 1.0.3
This patch was released worldwide on October 27, 2014. Conquest mode will no longer display the current results of the Conquest in progress. The update includes a slightly different mix of the Battle! Reshiram / Zekrom song for the N's Castle stage as well. It also addresses other minor issues that have not been specified.
So according to that, music can change between patches? Now to patch those shortened songs pretty please, Sakurai.