I have two separate Wilson lines in my ancestry, one from Co.Offaly here in Ireland the other from England (Huntingtonshire, Lincolnshire and Yorkshire) , none from Scotland
I couldn't find nothing else for possible matches to Owen and Margaret or their son Thomas unfortunately, but it's worth rechecking for spelling variations, wider date range etc.
Many of the records for the City area are on the free IrishGenealogy website, and transcripts of a number of the parishes in Co. Dublin are available on the RootsIreland pay website (mostly RC and Church of Ireland or both these sites)
Owen could be spelt the Irish way - Eoghan or Eoin, or in Latin in parish records if they were Catholic i.e. Eugenius, possibly also worth trying variations in spelling for the surname also - e.g. Gaghan/McGaghan etc
It's possible that they lived in a parish where records dont go back far enough, or were noted on now lost/damaged pages in the registers, or where records are not avaialable online. If a more detailed location crops in any of later Scottish records, e.g. the name of a town or parish in Co. Dublin , then you could possilby try a more focused search