Details of Charles McBride’s parents should be on his 1886 Scottish death certificate, which you can view on the Scotlandspeople site. In addition, the certificate should tell you whether they were alive at the time. (It will say “dcd” if dead. If that isn’t there, then you can infer they were alive. Scottish Registrar’s were pretty meticulous about that).
If you let me know what the certificate says about whether they were alive or dead, and what John McBride’s wife’s name was, I’ll then advise how to search for their deaths, though if they died before 1864, there won’t be any record. Death registration only started in Ireland in 1864.
You say that the McBride family was RC. Milltown is in the RC parish of Ardstraw West. Their baptism & marriage records only start in 1846. So assuming that’s where John McBride was born, there won’t be a record of it. But you might find his marriage if it was 1846 onwards.
You ask what happened to Samuel after his parents death until he left for Australia. An orphanage is one possibility. (The big orphanage near Johnstone was Quarrier's Homes. I think their records have survived. They might be in the Mithcell Library in Glasgow). Another possibility is that he was sent to stay with relatives. Typically an aunt or uncle or with his grandparents. 12 is a bit young to have started work full time. That was more likely when he was about 14 or 15.
You are curious as to why the family went to Scotland. Ireland lacks natural resources. No coal, oil, iron ore etc, and so apart from a modest amount of shipbuilding in Belfast and the Belfast linen mills (which mostly only employed women), it did not really get the industrial revolution that benefited England and Scotland where mills, steelworks, ship building, coal mining and all their support industries were major employers creating hundreds of thousands of new jobs. Much better paid than subsistence farming or weaving. Added to that you had the effects of a massive population explosion in Ireland – up from 3 million in 1750 to 8 million in 1841 (no-one is really sure of the reasons why but reduced neo-natal deaths seem to be a factor) and the famine. So some push factors and some pull factors saw huge numbers of people leave Ireland. Something like 8 million people emigrated from Ireland between 1801 & 1921.
If you look at the Scottish censuses for the Glasgow area in the late 1800s, you will see that about every fifth person recorded there was born in Ireland. Scotland was a particularly popular place to go to work because it was easy and very cheap to get to. Several sailings every day from Belfast, plus regular sailings from Portrush, Ballycastle and Londonderry. The shipping companies main business was cargo and the passengers were just top-up revenue. Competition was fierce and passenger fares very low. People working in Scotland could come home for weddings or the harvest, as well as holidays (Glasgow used to shut down for 2 weeks every July, known as the Glasgow Fair holiday and there would then be a huge exodus to Ireland). You could also send children back to stay with their grandparents, thereby leaving the wife free to work. You couldn’t do all those things so easily from Australia, America or Canada.