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I have upon your advice ordered the printout version of the death cert. I hope it's worth it!

FYI
https://www.rootschat.com/forum/index.php?topic=157902.0
You might think about the information that is possibly on the death certificates for Mary’s parents.

Have you seen the marriage record? It might give you information about a previous marriage. It is possible that Hugh and Donald were from another marriage.

I note that on Mary’s birth record 05/09/1840 Kilmarnock she is recorded as the fourth child of Alexander McDonald. So there must have been another older sibling (who died) in addition to Hugh and Donald.
Do you have the McDonald-McLean marriage record to see if this was the first marriage for both parties?
MCDONALD   ALEXANDER   marriage to AGNES MCLEAN       FR2642 (FR2642)   
15/09/1835   597/    110 163   Kilmarnock

Have a look at the passenger list for the EBBA BRAHE arriving Melbourne Dec 1857 from Liverpool.
There are the following scots: Alexander and Ann McDonald , both age 46, and Mary McDonald age 16.
His occupation is just “factory” – which may have been the case. Most of the Ayrshire cotton workers were in factories by this stage.
Mary is listed separately in single women – Her age is slightly out, but she may have reduced her age for a cheaper passage.
This is in the un-assisted passenger listing.
https://prov.vic.gov.au/archive/3B0750BA-F96C-11E9-AE98-19084F8A768F?image=278

...  however gives wife's name as "Agnes" - which I know is going to cause heated debate .....

Not at all - "Agnes" = "Ann" = "Nan" in Scotland and other places in between.

Please, a little more detail….
Where and when was Mary born?
What was her mother’s maiden name?
Where was the family in the 1851 census?
Is this the family in 1841?
https://www.freecen.org.uk/search_records/5a1424a4f4040b9d6e0f043f/alexander-mcdonald-1841-ayrshire-kilmarnock-1801-?locale=en

Added. The family in 1851. Mary’s age mis-transcribed? - should be 12
https://www.freecen.org.uk/search_records/59027c57e9379091b1227c62/alex-mcdonald-1851-ayrshire-ayr-1802-?locale=en