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Turns out when I tried a completely fresh project for the entire thing, the exported clothes work fine. (I should've done this to isolate the problem first sorry!)

So whatever is causing it is entirely on me and my edits haha, worst case if I can't figure out what I've done I'll just restart it and build it all up again in an afternoon.

But thank you for the help offer and sorry to bother you with this!

Is the VRC_FaceSmoothing.py equivalent to your vrc.py mentioned in the shark base for exporting the clothes again from blender as a preset?  

The avatar breaks if I try and export from blender and add the clothes to the unity hierarchy if the armature is included, though I'm probably just doing something silly. 

But if you have any hints that may help I'd appreciate it!