Substance Designer users: I gather it has some features that aren't really easily replicable in pixel shaders. Like, e.g. applying a sharpen filter? Is that true, I've not really used the program.
It's more of a tool to generate textures than it is anything to do with shaders. While I'm sure you can change the shader it uses, it's really kind of made to plug directly into the standard shader in Unity/UE/whatever.
You can either start out with an existing image and modify it from there, split it out into various PBR maps (albedo, roughness, metallic, etc), or you can procedurally create the texture using various shapes and noises, and layer on effects. The procedural texture approach is really cool, because you can modify the seed value used to generate them at runtime- and because they're built by algorithm instead of pixels, they're really small on disk, and scale to any resolution.
Using the program to actually make anything this way is kind of an artistic skill on its own, but it is fun.