I think I've finally solved the enigma... I thought about it after reading some of the links tater posted.
The pack I took the skins from (NYGM, by the way) had a different
NDD soldati.dat file, despite the same name as the one in WDAD or OM. The 3D model is the same, but seems like the way it handle the textures is different. I added that .dat to the pack with the textures and... voilá, in the first mission I loaded there were four destroyers with 2 different textures

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