Amadeus sees connections of less than 24 hours as a transit typically (as per typical transit ticketing rules), so it would've thought MEL as your destination but then realised your stop in MEL is only 1 hour so offered to check you in for all 3.

It's a bit weird to be honest.

A same day SYD-MEL-SYD clearly has a destination of MEL - it's obvious when there's only 2 sectors.