That would work only for a planar distribution of material. A 3D distribution would require multiple layers (I guess it might quickly become infeasible if it requires thousands of layers).
In the case of 3D arrangements, I think some substrate materials (and also some properties of the particles) would be very difficult to get using photolithography (or some kind of micro 3D printing).
In the case of 3D arrangements, you don't necessarily need to create all the layers photolithographically. You might be able to flatten N layers into 1 layer, then add a plastic coating equivalent to N-1 layers ontop, then repeat that. You'll have a very similar result to every layer being separate.
Imagine e.g. the "multiple layers of cardboard cutouts" scenery in theater vs it actually being 3D.
In the case of 3D arrangements, I think some substrate materials (and also some properties of the particles) would be very difficult to get using photolithography (or some kind of micro 3D printing).