You can bake maps from the geometry such as Curvature, Position , AO which you can then use in driving the nodes to create your material. When you publish the material, you do so with bitmap nodes replacing those specific maps so that the material works with other geometry.
This is how such materials work in Painter. You import the geometry, bake the maps, then the materials use those maps as an input.
One way I could think of is to use vertex painting on the mesh to identify the required vertices, in your modelling application, prior to linking it in Substance Designer. Then after linking the mesh, bake a colour map from the vertex colours. That would give you the location of those specific vertices on your material from which you could drive the cracks.