Important to note, the preponderance of the evidence supports Madison never changed his views. In his childhood he had witnessed the persecution by the Anglican establishment, and therefore had a strict view of separation of church/state relations, voicing his opinion vociferously at Princeton. This view never left him--even after he retired. These separation views should not be construed to conflict with his faith in Jesus Christ; The One he believed is God:
Gospels.-Madison's "Notes on Commentary on the Bible" found in The Papers of James Madison, p. 51-59. Vol. I. 16 Mar 1751 - 16 Dec. 1779. Edited by William T. Hutchinson and William M. E. Rachal. 1962, by the University of Chicago Press.
Mat. Ch 1st Pollution[:] Christ did by the power of his Godhead purify our nature from all the pollution of our Ancestors v. 5. &c
"Omnisciency--God's foreknowledge doth not compel, but permits to be done." Acts, ch. II. v. 23.
"Christ's divinity appears by St. John, ch. XX. v. 28."
"Resurrection testified and witnessed by the Apostles. Acts, ch. IV. v. 33."
As I mentioned earlier in this post, there is no substantial evidence that James Madison changed these beliefs: The Deity of Christ, Tri-Unity of God, Original Sin, and Pre-destination. If there are, they haven't been discovered yet. His writings about separation doctrine begin at Princeton University; at that time, the most Orthodox Seminary in the World.
Now that we understand not to confuse his views on separation doctrine with his faith, let us look at the minority evidence against James Madison's Orthodoxy. Here is James Madison in an address to the Cherokee Indians in 1812:
The Great Spirit has given you, like your white brethren, good heads to contrive, and strong arms, and active bodies. Use them like your white brethren of the eighteen fires, and like them, your little sparks will grow into great fires. You will be well fed, dwell in good houses, and enjoy the happiness for which you, like them, were created. These are the words of your father to his red children. The Great Spirit who is the father of us all, approves them. Let them pass through the ear in to the heart. Carry them home to your people; and as long as you remember this visit to your father of the eighteen fires, remember these are his last and best words to you!This statement can barely prove Madison retracted his views of Christ; His name isn't even mentioned. Furthermore, JM wrote all other religions besides Christianity were false:
The first is an arrogant pretension falsified by the contradictory opinions of Rulers in all ages, and throughout the world: the second an unhallowed perversion of the means of salvation...Because the establishment proposed by the Bill is not requisite for the support of the Christian Religion. To say that it is, is a contradiction to the Christian Religion itself, for every page of it disavows a dependence on the powers of this world: it is a contradiction to fact; for it is known that this Religion both existed and flourished, not only without the support of human laws, but in spite of every opposition from them, and not only during the period of miraculous aid, but long after it had been left to its own evidence and the ordinary care of Providence. Nay, it is a contradiction in terms; for a Religion not invented by human policy, must have pre-existed and been supported, before it was established by human policy. It is moreover to weaken in those who profess this Religion a pious confidence in its innate excellence and the patronage of its Author; and to foster in those who still reject it, a suspicion that its friends are too conscious of its fallacies to trust it to its own merits...Because the policy of the Bill is adverse to the diffusion of the light of Christianity. The first wish of those who enjoy this precious gift ought to be that it may be imparted to the whole race of mankind. Compare the number of those who have as yet received it with the number still remaining under the dominion of false Religions; and how small is the former! Does the policy of the Bill tend to lessen the disproportion? No; it at once discourages those who are strangers to the light of revelation from coming into the Region of it; and countenances by example the nations who continue in darkness, in shutting out those who might convey it to them.-Memorial and Remonstrance, June 20, 1785.
Here, is another account referring to JM's heterodoxy:
I found the President more free and open than I expected, starting subjects of conversation and making remarks that sometimes savored of humor and levity. He sometimes laughed, and I was glad to hear it ; but his face was always grave. He talked of religious sects and parties, and was curious to know how the cause of liberal Christianity stood with us, and if the Athanasian creed was well received by our Episcopalians. He pretty distinctly intimated to me his own regard for the Unitarian doctrines.— TICKNOR, GEORGE, 1815, Letter to his Father, Jan. 21 ; Life, Letters and Journals, vol. I, p. 30.
The problem is these words are not from the pen of James Madison, nor do they refer to the person of Jesus Christ.
Lastly, Madison refers to an Arian, Samuel Clarke, while defending God created the universe:
I have duly recd the copy of your little tract on the proofs of the Being & Attributes of God. To do full justice to it, would require not only a more critical attention than I have been able to bestow on it, but a resort to the celebrated work of Dr. Clarke, which I read fifty years ago only, and to that of Dr. Waterland also which I never read..But whatever effect may be produced on some minds by the more abstract train of ideas which you so strongly support, it will probably always be found that the course of reasoning from the effect to the cause, "from Nature to Nature's God," Will be the more universal & more persuasive application.-To Frederick Beasley (Nov. 20, 1825), in 9 The Papers of James Madison, 1819-1836, at 229 (Gaillard Hunt ed., 1910).
Again, no mention of the person of Jesus Christ. He had not read Clarke in fifty years, which would be 1775, a time when he was affirming Pre-destination to his Presbyterian friend, Stanley Stanhope Smith! Hardly evidence rejecting Orthodoxy. It could be Madison never knew Clarke was an Arian. Also, the context of the quote is The God of Abraham, Isaac, and Jacob, given JM quotes the God of the Bible, whom the Founding Fathers, and Christian philosophers, including: Francis Bacon (Thomas Jefferson's idol), Montesquieu, Blackstone, et al. penned as "Nature's God."