The Documents/My Games/GC2TwilightArnor folder has a pre-generated Gfx subfolder, suggesting the ability to add and/or replace textures without using mods (which break Metaverse compatibility) or replacing in-game files. I suppose though it's there mainly for customizing civilizations, which don't need mods to work.

Music apparently works the exact same way: I've been able to switch vanilla tracks with GalCiv3 music by creating Music and Event Music subfolders and adding MP3 files named identically to the vanilla ones (though I had to repurpose a few factions' diplomatic themes as background music).

There is apparently an issue though: I think GalCiv2's music system was meant to work with constant bitrate MP3 files, and I used some variable bitrate files from GalCiv3's official OST (as opposed to ones actually used by GalCiv3, though I used them too). When switching from a screen with different music, the VBR track rewinds by a some timespan backwards (i. e. one part of the melody is played again). I haven't tested replacing those tracks with CBR versions yet.