I think it is the same man, your James. Signatures are very similar and distinct particularly for the form of some of the letters.
You are right. The signature for James Smith son is from him being the informant to his mother's death in 1864. You have seen that it was sister Agnes, who lived with parents for many years, who reported her father John's death in 1866.
The second signature with James as father is from 1861 and James reporting on the birth of his daughter Janet.
So, would be pointing towards confirmation that your James's parents were John Smith from England and Agnes Walker from Ireland. Can't say it will be easy for you there
Cannot see any births for their children in Scotland but many people did not register or christen their children. Also, many registers have been lost or destroyed over the years. Only about a third of events are to be found in the OPRs. Even less if the family did not belong to the established Church of Scotland.
I have seen one marriage that could fit and looked at the parish register entry image but nothing there really to confirm whether it is the correct entry for John and Agnes. Their signatures are included...but can't think for them what to compare them with!
The marriage I saw is this one
www.familysearch.org/ark:/61903/1:1:NL4Z-P35 With John Smith showing as born in England and Agnes in Ireland, they could well have met in England but made their lives in Scotland.
Monica