I don't know if you are aware of this connection, but William McKee's (d. 1823 Mifflin Twp.) daughter Ann (b. c.1784, living 1870) married James McGowan (c.1781-1851).It looks like James may have been a brother of John B. McGowan, father of Zeruiah.
Your McKee line seems to go through Robert McKee (d. 1828), of St. Clair Twp., who in all likelihood was William's brother.
I wouldn't put much stock in that website, although the book _McKees of Virginia and Kentucky_ has some very interesting and valuable letters, suggesting earlier relationships.
As it stands now, the closest likely relatives of David McKee (d. 1795), besides his children, seem to be the above Robert, William, and Guian.There are many reasons to link them.So most likely their father was David's brother.David's daughter Margaret could be William MCKee's wife Margaret, if the wording in David's will is such that he intends to indicate that Margaret was married to a McKee----it's the same wording as the daughter Mary Pebbles.