I've noticed that a lot of people have differing interpretations for what words mean. Sometimes they have a range of meanings, depending on context. I can see someone using "Atheist" to describe someone who is against Christianity, but it's not quite right. Many of us are guilty of imprecision in our speech from time to time, and so I often consider statements to be of a general nature, showing a range and a direction, and not necessarily being precisely accurate.
As to Mr. Lincoln’s religious views, he was in short an infidel, was a universalist, was a unitarian, a theist.
I've seen that quote attributed to Stuart. Which is correct?
As time went on, Herndon took up with anti-religious circles, and that colored his view of Lincoln.
Could be. People often want their own views to be seen as popular among admired people, and so here perhaps is why this man would want Lincoln to be seen as agreeing with his own opinions. It boosts Herndon's perception of his own importance and wisdom.
Sources I've seen say it was Herndon and that he wrote it in a letter to a freethinking magazine.