The music, graciously provided by Vinzent Spielmann and Hannah Matthay, is divided into tracks. From there on I can separately adjust each track's volume, to fade them in and out at will and create the mood I'm after. This will be able to happen programmatically, using the same node-based trees as the game logic uses.
The way that I'm keeping each track synced up is by, as a song in playing, always having all tracks play at all times, and only muting the volume is I want one turned off. That way, when one need to return, it'll have kept it's tempo and join back in at the right time.
One of the repercussion is that, to control each track separately, they all need to be separate audio sources playing in Unity. This is handled by generating empty game objects for each song and then adding the audio source components to them, and the tracks placed in those sources. They are then linked back to the controller script.
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I'm busy working on my blog posts. Watch this space!