Yes, ACC do not refund TRS into customers current accounts. They apply it to your loan each month, which has the effect of decreasing your repayment installment.
So instead of having a debit of the full repayment amount each month from your current account & a credit for your TRS amount, they just debit the net amount from your current account.
It doesn't really make any difference, apart from the fact that you dont actually physically see the exact TRS amount being applied until you get your loan statement. No matter what way it's done the TRS amount is still being applied to your loan, as you would have paid the larger amount out of your current account anyway, so basically the only difference is you have one transaction instead of two on your current account.
I presume the reason they do it this way has something to do with the way their computer/accounting systems are set up.