Blake and Paine both applied their reason to reading the Bible. They both learned the facts, became acquainted with the characters and committed the stories to memory. Paine saw all the faults in a document which had been assembled over hundreds of years. But Blake progressed beyond that to the stage of discerning the spiritual insights to which the assorted material included in the Bible points. He saw the importance of the failures and disappointment portrayed in biblical accounts, he saw patterns which were repeated for the sake of mastering the lessons which need to be learned, he saw individuals whose spiritual development were examples for others to follow in spite of their missteps.
It appears that Paine received the Bible literally and wanted to discard everything which he could not explain, understand or replicate. But when he looked past the written scripture, he found truth everywhere he looked as indicate in this quote from Age of Reason:
"That which is revelation to me, exists in something which no human mind can invent, no human hand can counterfeit or alter.
The Word of God is the Creation we behold; and this word of God revealeth to man all that is necessary for man to know of his Creator.
Do we want to contemplate his power? We see it in the immensity of his creation.
Do we want to contemplate his wisdom? We see it in the unchangeable order by which the incomprehensible whole is governed.
Do we want to contemplate his munificence? We see it in the abundance with which he fills the earth.
Do we want to contemplate his mercy? We see it in his not withholding that abundance, even from the unthankful.
Do we want to contemplate his will, so far as it respects man? The goodness he shows to all, is a lesson for our conduct to each other.
In fine — Do we want to know what God is? Search not the book called the Scripture, which any human hand might make, or any impostor invent; but the scripture called the Creation."
That Blake was satisfied with Paine's declaration of his personal experience of God is clear in Blake's final note on Watson's book.
Annotation to Watson, (E 619) "It appears to me Now that Tom Paine is a better Christian than the Bishop I have read this Book with attention & find that the Bishop has only hurt Paines heel while Paine has broken his head the
Bishop has not answerd one of Paines grand objections"
Wikimedia Commons Drawing for Pastorals of Virgil Thenot and Colinet Converse Seated Beneath Two Trees