In OpenMC, the root universe does not need to be given an id of 0 like in other codes (e.g., MCNP). Instead, OpenMC determines from the input which universe is the root, or “real world.” Since this input has multiple universes that are not nested below other universes, OpenMC cannot tell which is supposed to be the real root universe.
To make this particular model work, you can just comment out the pin-cells in the “pin-cell construction” section that are not part of Universe 3. This way, OpenMC will be able to decipher that universe 0 is your root.