such as DUS-LHR-SYD and CDG-LHR-SYD, were actually cheaper with BA to book from other sites, the the LHR-SYD route direct, or MAN-LHR-SYD

This is often the case with the big carriers and certainly not unique to BA. It has taken me only a few minutes to find similar examples on KL LHR AMS LAX, AF LHR CDG JFK and LH LHR FRA HKG, as compared to AMS LAX, CDG JFK and FRA HKG direct.

Although primarily intended, as you rightly say, to encourage people to transit through the airlines hub, it is very common for regular business travellers to take advantage of this by buying the best combination of tickets for their business trips to DUS and SYD to use your example, or LON and LAX to use one of mine.

1L