Thank you Westward and Maggsie for the additional information - it was very interesting! I hadn't realised, Westward, that early Victorian records turn up on NSW BDM. Learn something new every day!
I wrote to Victoria BDM to find out how they would explain any differences between the two records. I used Timothy Ahern and Ellen Mulcahy's marriage records from 1842. This is their reply:
"Please note that in 1842 the colony of Victoria was not yet in existence and the area known as Melbourne and its surrounds was part of the Port Phillip District, a special district of the colony of New South Wales.
Record number 286 is part of a list that was provided from the relevant churches detailing marriages that occurred in the district, the record 35459 is a record of marriage from members of the Roman catholic faith, it has a few more details than the list entry but please note that even compared to marriages that would be registered in the decade following it still maintains limited information."
...So, it appears if I were to order from the Vic BDM, I would order the 35459 record. However, Westward's suggestion of ordering a NSW transcript sounds eminently more sensible.
Thank you, everyone, for your help!