Its not Maya 2016, just the 2016 fbx exporter. You could select an older year. Also make sure the fbx exporter does not have Split per-vertex Normals checked as that will cause hard seams on your lowpoly.
Hmm! I'm actually using Maya 2016, so maybe that's the issue. Though I was able to reproduce the same problems through baking with XNormal (though the model was the same fbx I used in substance). Maya 2016 is all I've got though, so I might have to just use OBJs or something if that's the case.
Your issue with your seams can be a number of things. I think it might be your tangents and bi-normals not matching up correctly. Make sure the lowpoly model you used to bake with is the same model you are applying the normal map to in substance painter. As a test, you should re-export your lowpoly from Maya or whatever 3d…