Both. You'll probably use vert paint, being cheap and effective way to blend materials, and probably masks, even if it's just a basic noise and gradient material function to break up vertex paint blending or height lerp from a height imput for example. Also don't forget decals on top of what ever solution you use.
Outside application and or plugin, probably best since some time has past to jot this issue down for a later date to review and look into for next time and just go ahead and manually do it, this is a good example of why planning ahead is important. Blender might help with this idk about blender to much though & jumping…
Have you looked at Adobe's site? Tons of great resources to get you going: https://substance3d.adobe.com/tutorials?software=Substance%203D%20Designer As just one example: https://substance3d.adobe.com/tutorials/courses/creating-a-tudor-house-wall
There was an example posted somewhere within that Twitter thread- I can't find it, though. They showed the version the generator recreated as something akin to a messed up VHS tape- huge blocks of random colors and structural corruption