When you first bring in your model, does it matter where you bake your maps? in your 3D package or Substance painter?
The first time I've done it in Substance painter (Texture set settings-> Bake Mesh Maps), it looks fine. Then I watched this allegorithmic video
https://youtu.be/jCKtmQr4bGUI saw that he did it in Maya.
Does it matter? do you get better maps in one or the other?
same question applies to when you want to re-project UVs in Substance painter and need to re-bake.