Haha yeah, interesting question to begin with if you look deeper.
And, totally messed up on my previous attempt, I fixed it now.
Modified the .eft so it uses the alpha from the duplicated .dds, awesome. Missed some HUEB's in the .eft passes. The way I have it now is, the MAIN uses the white alpha of the original .dds for palette 1, and then made a unique 4 letter name tag for the second duplicated texture that uses the black part of that alpha, for palette 2.
I'll 100% confirm it tomorrow when I'll install my .dds plugin again, to be sure it's working, but I'm fairly confident it works, if I load the stock .eft it blacks out again.
Hope it actually skips the black alpha on the first and white alpha on the second though, that I need to verify with .dds editing. It should, but no idea if it does in reality, since it wasn't meant to do that, but we'll see.
This should enable better texture mods for double palette stuff without completely redoing the UV.
If this really works, I'll make a guide tomorrow and upload the modified .sht/.eft for ya Ahmose.
Edit:
DAMN IT, it doesn't work, still pulls the same alpha of MAIN. So apparently HUEB is irrelevant as a command, it's just a name that gets used, the mechanic of it using a white/black must be hard coded then if there is more than one in the TFNS0000. Ugh.
Edit 2:
Further research, I noticed that the belt (Using jacket_s17 to test 2 color stuff, don't have access to a factory for suits) used a different shader, even though there is just one texture. So now I see that I was wrong on how it's handled when there is more than 2 palettes. Basically, in the .MGN, you can 'select' parts of the UV/.dds and assign a .sht to it, meaning, you can have multiple shaders for one texture without having to actually split up the textures into different pieces in order to get different effects, I assume this would also work if you layer/overwrite some things.
Problem being, it needs the full coordinates for that area on the .dds, so unless I or someone else writes a tool for it, you can forget about it.
I tried everything I can think of in the .eft, to make it target the second .dds, but haven't had any luck.
@Ahmouse, do you want a single palette shader/eft, then? I can most likely do that, so it only uses the main color for the whole suite, that way you can use black to stop the palette from interfering with the emblem, any other colors would have to be done on the texture itself.