Hello,
As Jeremie mentioned the seams are fixed in an upcoming build of Substance Painter. I have attached a substance I use for padding textures. It works off of the shells of the UV as indicated by the alpha. If you supply a diffuse texture with alpha, it will pad it. However, if you enable "Use Mask" you can supply a mask that indicates what needs to be padded.
Cheers,
Wes