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They should be able to check bags through based on presentation on a valid connecting onward booking on the same airline. This is purely a "link" between two bookings and is not a merger of the two bookings into a single booking.As far as I'm aware they can't do that. Could be wrong though, never been game to try it.
This is not quite the full story. While it is true that visas are the passenger's responsibility, there is an obligation on the operating airline to ensure they only allow passengers with valid visas or exemptions for the destination country to board an international flight. If an airline carries a passenger who does not have the proper visa or exemption and that passenger is denied entry and deported, the airline is fined and also has fund the return journey (they may ask the passenger to reimburse the costs).Still doesn't seem like a reason to cancel your booking. Visa issues are on the PAX, so QF wouldn't likely care if you had one to enter Japan or not.
Note that it is not a requirement that the onward flight is on the same booking/itinerary. So presenting an onward flight booking that meets the requirement for transit exemption for a Visa would be perfectly acceptable to the airline for the purpose of allowing boarding the flight, as it would be for immigration officials at the transit country.