This was an issue in 4.2 as well but you told me only to bother with a bug report once I updated to 4.3, so here you go Nate 😛
The nice thing about the 4.3 update is that it actually fixed what I assume was a problem on the unity side of things (visual errors with meshes when the multiply layers existed). However the other half of the problem is still there (though admittedly it may ALSO be entirely a unity runtime error as well). So here it is:
When exporting with pack settings that include multiple outputs (in my case 2 scales) on a file that contains non-normal blending modes (multiply) only one of the two outputs creates materials in unity with multiply (I assume this is controlled by the atlas or the json but wasn't sure which so don't want to assume).
I'm unsure what dictates which of the two atlas/textures is decided as the default to attach to the skeletonData when importing, but interestingly whichever one it is is the one that actually gets the multiply materials added. The other one is treated as though all slots had normal blending, which causes some obvious issues when those slots were intended to be multiply layers. I'm also not 100% sure but it seems like at least additive blending mode does not require separate materials be made, so this may only effect multiply (I don't use screen for anything so possibly that too).