I basicly wanted to ask the same question as Scooby, as another Painter user but due to lack of time for establishing proper Painter -> FSO workflow, well... I guess it's about time to join the discussion.
Normalmaps from Painter are inverted by default in FSO, as they are in DirectX normalmap format. Export them with no alpha, disassemble on separate red, green and blue channels, than invert green and blue. Set red as alpha, and assemble normal again. As for DDS formats, everything with alpha is DXT5 and without alpha is DXT1. I'm not sure if FSO handles any mipmapping.
Additional maps like team colors may be handled by -misc by FSO engine.
Is there any easy way to convert metal/rough to spec/gloss? DahBlount was explaining me this on discord channel, but I was tired as hell and now I remember nothing o___O.