This article is valuable for showing in great detail that not even Jefferson held the position that has been created by modern constitutional jurisprudence misusing his "wall of separation" phrase.
But what is more basic is that this phrase and the "Danbury letter" was an ABSURD place to go prospecting for the meaning of the 1st Amendment. As you both have noted, Jefferson was not part of the Constitutional Convention and was not even in the country. Also, as the article notes near the beginning, he was far from the spokesman for his contemporaries on all matters of religion and state and in fact was regarded as having views on the margin of society in that regard. Thus, for Justice Black and others to rely upon a MISREADING of Jefferson to create a fictitious intellectual pedigree for the supposed original meaning of the 1st Amendment is just the usual sort of liberal FRAUD.
Nearly every one of the original 13 states had an ESTABLISHED religion during the presidencies of George Washington, John Adams, and Thomas Jefferson, so whatever the 1st Amendment was intended to do it certainly wasn't meant by anyone as a bar to any (state and local) government support of Christian religion, it was meant simply to keep the federal government from creating a national establishment of one Christian denomination over the others.
Full agreement...