Actually, Painter supports a Non-PBR (Diff/Gloss/Spec) workflow out-of-the-box, all you have to do is set it up in the project settings, or even when you export the PBR maps you paint, you can convert them to non-PBR on export, since painter lets you choose which channels to export.
you'll need to find a last-gen shader for substance designer to use it to texture models for skyrim - as skyrim doesn't support the PBR material approach to convert the .nif files into .obj or FBX you could use Noesis