You're right Scharyn it is a very confusing family, and maybe I'm going to confuse you more.
In Trove, there is a list of Unclaimed Letters from 31 March 1854 and there is 'John or Thomas Mulvihil', so maybe he went by both names or they were brothers?
Some transcriptions of death records in South Australia in the FamilyHistorySA website also have the death of two children at Dry Creek with what I presume is the father's name of Thomas
MULVIHILL John died 1853-06-27 aged 8 d at Dry Creek; relative/informant Thomas (F)
MULVIHILL Mary died 1853-06-30 aged 12 d at Dry Creek; relative/informant Thomas (F)
I'm presuming the (F) stands for father?
I don't know if you have seen the actual marriage certificate for Bridget Julia Mulvihill or just a transcription, but I'm wondering if the father's name Sam might actually be Tom? That would cut the father's down to only two?
My best guess would be that the father was Thomas John, preferred name John or John Thomas? Or the father's name was Thomas and the obituary got it wrong.
As I said I've probably made the confusion even worse.