It's very possible that Substance Painter can also edit the UV map, but I'm not sure.
But! I messed up the transparency xD
I did this: I took the DDS from the data folder (Substance refused to open it, and it's an old DDS DX_T_3), so I opened the DDS in Photoshop, saved it as PNG, Substance opened it, everything was fine, I changed the colors for the hero (so it wouldn't be confused with monsters), exported it as a Targa from Substance, converted the Targa to DDS DX_T_3 through Photoshop, and put it back in the data folder.

Why is it red? (because the specialization is fire ball).