Hi all, Substance user here.
Yes, Substance Painter does its magic with UV maps, and most of the workflow is based on mixing layers with grayscale masks (pretty much what @Michael_W described above), so actual “painting” typically happens to the mask texture most of the time, and not directly to N channels. This way the whole workflow remains non-destructive: amending a grayscale mask is way easier than erasing stuff across roughness+basecolor+height channels.
What makes substance painter special is its “smart masks” (e.g. dirt, soft edges, dirt from ground, etc, etc) which are in fact a simple-ish mix of some of the baked textures (curvature map, world position map, etc). Aaand… to my surprise Blender has excellent support for those as well with Geometry node (e.g. pointiness output which is basically Substance Painter’s curvature map).
And, of course, SP offers a lot of procedural textures, which I miss a lot in Blender. Overall, I find the approach of painting the mask texture fairly acceptable — basically because I don’t actually do too much painting with SP