I think you are right to doubt the relevance of the Auchterarder or Logie burials as being the one you are looking for. Never trust anything you find online, and especially anything you find in an online tree on Ancestry or similar web sites, as you have no idea where the information came from.
I see that Scotland's People has only one baptism of a child to James D and Christian Blyth*; David, baptised 1780 in Scone, but there are baptisms there of numerous children to James D, no mother named, including two Margarets, one in 1765 and one in 1773.
You can safely dismiss the Kinkell/Auchterarder/Trinity Gask stone. The eldest recorded child of James Donaldson and Helen Sm*ton was Janet, baptised in 1774 in Trinity Gask. As this is six years before the baptism of David to JD and Christian Blythe's youngest child, the families overlap, therefore Helen Smitton is not a second wife of your JD, and it follows that the Kinkell/Auchterarder grave inscription is a red herring.
I can't comment on the Logie one, but it does seem unlikely.
I see that there are 207 recorded burials of James Donaldsons from 1780 onwards, of whom 18 were in Perthshire. As there are 526 recorded baptisms of James Donaldsons before 1780, there are obviously plenty of unrecorded ones.
Have you looked at the JD who was buried in Scone on 3 September 1780? And have you looked at the baptism of David D in Scone on 22 August 1780? Does either record contain any useful additional details?
Only a small proportion of gravestones are on FindAGrave or elsewhere online. There are only 74 people buried in Old Scone on FAG.
Assuming that the JD who died in Scone in 1780 isn't Christian Blythe's husband (or even if he is), it is possible that there is a stone in Scone old kirkyard commemorating a JD who died on 13 September 1795. You need to follow up all the references on the Ancestry trees until you get back to one that isn't just a copy of another one, and then find out where that tree's information came from.
There are booklets of pre-1855 monumental inscriptions in Perthshire, available from
https://tayvalleyfhs.org.uk/ or
https://www.scotsgenealogy.com/