The Memorial is filled with declarations for the truth of Christianity, that is, the orthodox beliefs held by the majority of Christians for hundreds of years.
"Whilst we assert for ourselves a freedom to embrace, to profess and to observe the Religion which we believe to be of divine origin, we cannot deny an equal freedom to those whose minds have not yet yielded to the evidence which has convinced us." James Madison, Memorial and Remonstrance, [ca. 20 June 1785] http://odur.let.rug.nl/~usa/P/jm4/writings/memor.htm
Madison is here, including himself with orthodox Christians, not infidel whigs, or anyone else. He is saying I am one of you. A key point to understand is the audience the seminary student is addressing; most, if not all those Virginians were orthodox Christians, as historian James Hutson notes, this document was “written to appeal to evangelical forces during a petition campaign in 1785.″ These evangelical forces were orthodox, the secret "infidel" whigs were not a threat. http://positiveliberty.com/2007/09/bishop-meade-on-james-madisons-creed.html
Another point to reflect on is Bishop Meade's comments on Madison's words for Christianity. When Meade writes,
"It is drawn up on the supposition of the truth of Christianity. It must indeed have done this in order to be acceptable to those by whom it was solicited." http://books.google.com/books?id=M0oOAAAAIAAJ&pg=PA305&dq=bishop+meade,+old+churches+volume+II+papers#PPA1,M1
Does Meade understand this comment as an attack against Madison not being truthful, or an obvious statement? I believe it's the latter; accusing Madison of being disengenious, lying to his family, and the people of Virginia just to defeat an assessment bill doesn't seem right to me. Even if Bishop Meade does believe Madison is lying to garner votes, does that seem to be Madison's character? The words Madison uses in the Memorial seem to be authentic, with a great deal of time and thought put into it:
"Because the Bill implies either that the Civil Magistrate is a competent Judge of Religious Truth; or that he may employ Religion as an engine of Civil policy... The second an unhallowed perversion of the means of salvation."
Madison is saying Christianity is the only truth, and Jesus is the only means of salvation. Earlier, he explained Christianity is true, and everything else false; again, do not be deceived about the Christianity Madison is talking about. He is referring to orthodoxy, not heterodoxy. Madison was no universalist at this time, and from the orthodox audience he's addressing, labeling him anything else is unreasonable as well. Here Madison wishes everyone would be a Christian:"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(Christianity) may be imparted to the whole race of mankind."
If another religion was adequate for salvation, Madison would never have said this. Again, Madison exalts Christianity over the other false religions; quite different from his "best and purest religion" comment in 1833. Madison again:
"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. Instead of Levelling as far as possible, every obstacle to the victorious progress of Truth"
As to the faith of James Madison after forming the nation, I see it as irrelevant; although, I firmly believe he abandoned Jesus Christ, and became a polytheist, as is current President, George Bush.