Substance painter unfortunately is nowhere near the level of performance when it comes to tweaking and painting as Mari.
Edit: In fact I would go as far as to say it is at this stage not production ready for that kind of a job,right now best method is to paint in Mari and add procedural elements in substance and then take it back to Mari in case of tweaks. Foundry know this otherwise the price tag on that Software wont sit so comfortably on nearly 2000 US