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Context is important is it not?

You cited “The civil Government, though bereft of everything like an associated hierarchy, possesses the requisite stability, and performs its functions with complete success, whilst the number, the industry, and the morality of the priesthood, and the devotion of the people, have been manifestly increased by the total separation of the church from the State (Letter to Robert Walsh, Mar. 2, 1819).”

as one of your examples and I am assuming you are saying Madison defined and supported the current liberal/progressive view of “separation of church and state” I believe. But when you read the full context you may see things differently. Specifically the line just before your quote “It was the Universal opinion of the Century preceding the

last, that Civil Govt could not stand without the prop of a Religious

establishment, & that the Xn religion itself, would perish if not supported

by a legal provision for its Clergy.”

Full Paragraph and link to letter below.

That there has been an increase of religious instruction since the

revolution can admit of no question. The English church was originally the

established religion, the character of the clergy that above described. Of

other sects there were but few adherents, except the Presbyterians who

predominated on the W side of the Blue Mountains. A little time previous to

the Revolutionary struggle the Baptists sprang up, and made a very rapid

progress. Among the early acts of the Republican Legislature, were those

abolishing the Religious establishment, and putting all Sects at full

liberty and on a perfect level. At present the population is divided, with

small exceptions, among the Protestant Episcopalians, the Presbyterians, the

Baptists & the Methodists. Of their comparative numbers I can command no

sources of information. I conjecture the Presbytenans & Baptists to form

each abt a third, & the two other sects together of which the Methodists are

much the smallest, to make up the remaining third. The Old churches, built

under the establisht at the public expence, have in many instances gone to

ruin, or are in a very dilapidated state, owing chiefly to a transition

desertion of the flocks to other worships. A few new ones have latterly been

built particularly in the towns. Among the other sects, Meeting Houses, have

multiplied & continue to multiply, tho’ in general they are of the plainest

and cheapest sort. But neither the number nor the style of the Religious

edifices is a true measure of the state of religion. Religious instruction

is now diffused throughout the Community by preachers of every sect with

almost equal zeal, tho’ with very unequal acquirements, and at private

houses & open stations and occasionally in such as are appropriated to Civil

use, as well as buildings appropriated to that use. The qualifications of

the Preachers, too among the new sects where there was the greatest

deficiency, are understood to be improving. On a general comparison of the

present & former times, the balance is certainly & vastly on the side of the

present, as to the number of religious teachers the zeal which actuates

them, the purity of their lives, and the attendance of the people on their

instructions. It was the Universal opinion of the Century preceding the

last, that Civil Govt could not stand without the prop of a Religious

establishment, & that the Xn religion itself, would perish if not supported

by a legal provision for its Clergy. The experience of Virginia

conspicuously corroborates the disproof of both opinions. The Civil Govt,

tho’ bereft of everything like an associated hierarchy, possesses the

requisite stability and performs its functions with complete success, Whilst

the number, the industry, and the morality of the Priesthood, & the devotion

of the people have been manifestly increased by the total separation of the

Church from the State.

One source is http://www.constitution.org/jm/18190302_walsh.txt