The problem is that substance never actually hides things from drawing. It will still draw on backfaces (even though they are not visible) and it still draws onto invisible UV Tiles. I think for now the only workaround is to use Mari instead, which is a shame given its price tag. :/
It may be possible to render out Substances brush strokes and reimport them as an image (basically exporting the masks and then reimporting them), which could also workaround your issue (but beware of seams between visible and hidden UV Tiles which you may need to fix later).