I believe my problem here was that I added the material IDs to the mesh in Blender, after initially importing the mesh into UE4, so I reimported it. Doing a reimport instead of importing it as a new asset (with a different name) for some reason does not work with "send to substance". I had to delete the asset from my UE4 and import it again, or import it with a different name and then I saw the material IDs.
Even though I got it to work, I ended up changing my technique to use color ID maps anyway because I need 1 material per mesh.