The answer to your question will depend upon the runway in use at Melbourne Airport(ML). If 27 is in use at ML you will not get a clearance direct from Kilmore to Essendon (EN) but you may get one at 1500 feet from Plenty Locator direct to EN. You will, most times, get a clearance at 1500 ft. from Albert Park, Station Pier or Westgate Bridge. Clearance via Rockbank is very rarely given. Clearances at higher altitudes can be requested from ML Centre but you should file a plan so Centre knows about you in advance.
Good luck with your flight.