Hey outtoplay,
I did a bit hand painting textures myself (not good, but it was hand painted, at least ; )).
You can definitely achieve something like that with just the basic brush and blending colours together. That's the simplest method I know for Photoshop artists.
Unfortunately, you can't use smudge brushes or so, because Substance Painter has none of those at the moment. You could find some Hand painting tutorials for Photoshop, though. Try to use these techniques in Substance Painter. They should work, indeed.
If you have experience already: Sorry, I can't give you further tips, because I never was good at hand painting

Best Regards