There are three substantial differences:
1) James McClure was born in South Carolina in 1785, after the end of the American Revolution. William Loughton Smith had been born in 1758, well before the Revolution began.
2) Given his father's subsequent naturalization before James left for England at the age of 10, he fell under the auspices of the Naturalization Act of 1802, which rendered James a citizen of South Carolina (and hence the United States) in Publius's estimation (contra Armstrong Jr.), based on the bare text of the Act in question (which did indeed have some defects based on its application).
3) However, Smith actually returned to the United States in 1783, at the age of 25: the precise age at when McClure had been arrested in France in 1810. (We can only speculate as to whether or not McClure would have ever returned to America had the Horizon not shipwrecked on French shores.) In contrast, by the time of the election in 1788, Smith had continuously resided in the United States for five years at least.
Now, with that being said: David Ramsey's objection to seating William Loughton Smith (who had gotten more votes in the recent congressional election; funny how history rhymes...) was his allegation that Smith did not meet the "seven years a citizen requirement" of Article 1, Section 2, Clause 2. However, as noted in Article 1, Section 5, Clause 1: ". Each House shall be the Judge of the Elections, Returns and Qualifications of its own Members..." Given that Smith had been born in South Carolina in 1758 and had only left in 1770, he had resided there for the first decade of his life; that by itself would have met the seven years' requirement.
And, as James Madison himself noted in reply to Ramsey: "It were to be wished, that we had some law adduced more precisely defining the qualities of a citizen or an alien; particular laws of this kind, have obtained in some of the states; if such a law existed in South-Carolina, it might have prevented this question from ever coming before us; but since this has not been the case, let us settle some general principles before we proceed to the presumptive proof arising from public measures under the law, which tend to give support to the inference drawn from such principles. It is an established maxim that birth is a criterion of allegiance. Birth however derives its force sometimes from place and sometimes from parentage, but in general place is the most certain criterion; it is what applies in the United States; it will therefore be unnecessary to investigate any other. Mr. Smith founds his claim upon his birthright; his ancestors were among the first settlers of that colony...What was the situation of the people of America when the dissolution of their allegiance took place by the declaration of independence? I conceive that every person who owed this primary allegiance to the particular community in which he was born retained his right of birth, as the member of a new community; that he was consequently absolved from the secondary allegiance he had owed to the British sovereign: If he was not a minor, he became bound by his own act as a member of the society who separated with him from a submission to a foreign country. If he was a minor, his consent was involved in the decision of that society to which he belonged by the ties of nature. What was the allegiance as a citizen of South-Carolina, he owed to the King of Great Britain? He owed his allegiance to him as a King of that society to which, as a society he owed his primary allegiance. When that society separated from Great Britain, he was bound by that act and his allegiance transferred to that society, or the sovereign which that society should set up, because it was through his membership of the society of South-Carolina, that he owed allegiance to Great Britain. This reasoning will hold good, unless it is supposed that the separation which took place between these states and Great Britain, not only dissolved the union between those countries, but dissolved the union among the citizens themselves: that the original compact, which made them altogether one society, being dissolved, they could not fall into pieces, each part making an independent society, but must individually revert into a state of nature; but I do not conceive that this was of necessity to be the case; I believe such a revolution did not absolutely take place."
But I'm not sure how the case of McClure calls into question Madison's defense of Smith. In both cases (if Publius was indeed Madison), he held that the 'defendant' (so to speak) in question should be held as American citizens, contra Ramsey and Armstrong. If it's the matter of Publius mentioning expatriation in McClure's case and not in Smith's, that's handled by the contingent fact that Smith had returned to the United States in 1783 and been practicing law since 1784. McClure had never set foot back on American shores since he was ten years of age.
Had McClure ever returned to America for any substantial length of time, I doubt the matter of expatriation would have been mentioned.
I would posit that the reason place was the most "certain" criterion of citizenship in the 1790s was that travel in and out of the United States was impossible for most citizens. Only the most wealthy (or ambassadors of the United States) could afford passage on sailing ships to England or France for a six-week voyage under hardship conditions. If someone did manage to obtain such passage, they would stay in Europe for years before returning to the United States.
As was the case with Smith, his lineage to the land was well-known. I would think that to be true of most people in the 1790s; the townspeople of any town in the United States would have known who begat whom through the generations (they used to document that in family Bibles), and so "land" was a proxy for citizenship by parentage, too (the "most certain criterion").
Note that from the quoted passage above:
"Mr. Smith founds his claim upon his birthright; his ancestors were among the first settlers of that colony..."
..."birthright" today is interpreted to mean citizenship at birth (born here), but the rest of the passage cites Smith's parentage as his "birthright;" his "ancestors were among the first settlers."
Given that people didn't travel far distances back then, "land" and "ancestors" were synonymous in practice.
-PJ