It is entirely possible that the Reg Gen Office :

Did not process the marriage registration

Did not receive the quarterly return
It was the clergy's responsibility to lodge the paperwork at a deputy registrar's office .... it did not need to be one nearest to the Church. If the marriage was at the Registry Office near to Balmain, it still needed to be in the quarterly return to HQ ...
The clergy would hand to the bride the loose decorative certificate on the day .... and he would keep the register record in tact and the loose leaf registry copy separate. So at least 3 sets signed. End of the quarter, forward the loose leaf copies to HQ.
The bride and groom marry 1903, bride's brother born 1907 ... even if that was her child that is still a lengthy time gap ....
Common law marriages have been recognised in NSW law matters since at least Macquarie era... and prompted much of the Colonial law.
JM