When I retired four years ago, school admin staff were still compiling attendance data for pass holders, to calculate the number of days for which subsidy was payable.
When the Opal Card is finally provided to students it would probably just allow entry/exist without any charge. If the cards are free then there is no need to link them to a payment system. The method of working out subsidy would now be automated based on tap on/off history.
The obvious method of dealing with Pensioner Opal Cards would be to link them to the holders pension account. The problem with this is that it may be legally impossible to do this as the card is a state government matter whilst the pension is provided by the Commonwealth and if the account holder refuses to allow a direct debit from such account there is probably no way of forcing them to do so.
A lot of pensioners already have difficulty using an TVM to obtain a $2:50 ticket at stations that do not sell tickets through the windows due to the fact they insist on punching in a destination. Getting pensioners to use some sort of top up system will be a logistical nightmare as many still rely on cash transactions and think debit cards etc are the work of satan. I believe some banks still provide a pass book to access a pension account due to this aversion to plastic.