For anyone else still experiencing this issue, it seems to be caused by trying to apply the DRM wrapper to the bootstrap exe instead of the actual application exe. Remember that UE4 produces two executables; the exe in the project root folder is just a small application to check for prerequisites and invoke the real application exe which is typically further down in the directory structure.
This error from the DRM wrapper is precisely what is expected from trying to sign the bootstrapper rather than the program executable.