Fare wise there is nothing to test, as they appear to have made it clear they are not going to remove the 'mode change penalty' from Sydney's ticketing system. So there is nothing special Opal has to do for Bondi Junction interchange passengers. Change modes, it's a new journey and a new 'flag-fall'. The 1 hour interchange time for joining journeys into trips for 'weekly reward' counting has already been tested.
opal.com.au says... "If you transfer between a bus, train, or ferry service, your Opal fare will be calculated separately for your train trip and your ferry trip. If your transfer is completed within 60 minutes, this is considered to be one journey for the purposes of the Weekly Travel Reward."... which indicates that a change in mode does not result in a new journey.
But yes, you are right - it is a new fare flagfall.
I wonder what happens if you do bus-train-bus.
Perhaps I'm deluded, but I expect/hope/pray that once the system roll-out has progressed beyond some critical point, they will remove the "mode change penalty" you refer to.
Failing that, as a distant second consolation prize, if you are going to charge a new flagfall for a change in mode, then at least make it count as a new journey.
Public transport fare increases get the general population very worked up (for concrete examples look at ... this thread!). With a reduction in mode change penalty there will need to be an increase in fares elsewhere to maintain revenue. Plus, at the same time you would probably need to address to some extent the disparity between bus and train fares (approx: bus $1.80 flagfall + 0.25 $/km, train $3.00 flagfall + 0.065 $/km, I can hear the sounds of the short distance bus users and the long distance train users sharpening the tips of their pitch forks...). So softly, softly...
Point to point "crow flies" fares on the bus... excellent.