Hiya,
The latest version of substance painter and the latest version of blender work great together, you can now bake all the maps direct in substance painter as well so no messing about getting that sorted and it’s really easy.
I ended up with a workflow as follows that works well.
Model and uv unwrap in blender, create high and low res mesh if required, use vertex paint to colour the final mesh where you might want masks for painting, make sure you have just one material per object you are exporting, this will get imported as the mesh set name.
Export from blender as FBX this maintains all the vertex colour information.
In substance painter import the FBX file, for each mesh set bake all the maps you want, it’s really quick and easy and they get auto allocated to the mesh, you can add a separate high res mesh for baking at this point if you like. The ID map is the one that bakes out all the vertex colours.
Get painting, use the id map for quick masking (you can mask by UV, mesh etc in there as well as required but I found vertex painting it first was really quick and easy)
Once finished export the channels as maps, create a material in blender to use them, you can also export stuff like the curvature map, thickness etc. and use those to create dynamic materials, dynamic edge ware etc in blender.
I’d never bother baking maps in blender now substance painter is so quick and easy, it also means like for the sand I worked at 2k so it was quick and then at the end quickly re-baked everything at 4k and set the doc size to 4k and substance painter recalculates all the strokes and you get proper 4k maps not just uprezzed (unless you have uses actual textures of cause that are too small instead of dynamic materials)
It’s one of the few program’s i’ve used recently that has an initial easy learning curve and is genuinely fun to use, I did try it last year with blender and didn’t get on with it was a lot of fiddling about with maps etc but now it’s so easy just hit the bake button and go 
Hope that’s useful!
Mark