ScotinEngland, you're welcome!
It's pretty clear that there was a bit of a Charles presence in the area over quite a period back to the 1650s (per IGI). Moving forward, John Charles & Katherine Rob in Portsoy had Katharine bpt 1-12-1737 and James 19-7-1740. More relevant though is that "Mr Peter Charles gardiner in Cullen & Jannet Portes" [sic] had Alexander born 17-3-1771 - he must be in the running to be your Alexander's mysterious father. It's significant that Peter Charles was upped in status by being called 'Mr'.
Several witnesses were also 'Mr'. The OPR image I have isn't very good but one of them seems to be Mr Thomas Duncan in Blairock - and that's in Deskford parish. Another is Mr John Duncan in Broom (in Fordyce parish). Both also witnessed children of James Young & Isobel Findlay (the gdparents fo your Elspet Young). In 1763 and 1764, for their seventh and eighth children, he too is suddenly elevated to Mr James Young, as are most of the witnesses.
I'm keeping track of all this, of course, in the hope that it might lead to me identifying the parentage of my Ann Young who was born abt1757. By rights, she ought to be a sister of your John Young (who witnessed one of her Geddes children in 1792), but I cannot see how she can fit. At present in my tree, my Ann Young is instead tentatively a niece (not a daughter) of your James Young & Isobel Findlay, being also a sister of an Alexander Young h/o Margaret Christie.
The Youngs are off-topic for this thread. I suggest, if you want to continue discussing Youngs you start a new thread and we go from there, alternatively send me a PM with your email address.
(I've nearly got sidetracked because one of my lines is Porteous in Midlothian, leading back to James Porteous & Jean Porteous who marr 8-8-1712 Inveresk...)
Re shoemakers, well everybody needed their boots, so there's nothing exceptional about Fordyce. It was neither a centre of boots, nor an industrial centre - just a local service. But Fordyce Academy was indeed reputed to be the best.