^ I can't comment on the tokens in particular because I have only used it a couple of times and it was all on their subways (so I don't know how they work on their buses), and they didn't seem all that efficient to me. But for RFID smartcards in general, the chips remember past trips, so it can simply deduct accordingly when you switch modes and have transfer credits, even across different fare structures. Boston did it for all transit modes, but they are all by the same operator and had the same fare structure anyway. HK did it for all modes run by all different operators - 3 bus operators, 2 tram operators, 2 (now 1) HRT operators, 4-5 ferry operators, jitneys, etc.
Once all systems are synchronized and all transactions done by the smartcards, there will be lots of flexibilities to play with the fare system, with free/discounted transfers eg from train to bus. Better yet, because HK's Octopus card is so widely adopted, you can have credits from riding transit enough times and apply that on purchases at supermarkets and cinemas, and vice versa.