You Want It Darker Lyrics

Lyric discussion by waleed1003 

Cover art for You Want It Darker lyrics by Leonard Cohen

I don't think he is not not-making peace with God and all. But, I think he does not like how christianity is shaped by humans throughout history: The message being our approach to God is WRONG. Giving his background and timing (approaching death), I am inclined to say he is doing so by reflecting what he learned from judaism and about God in general. He is criticizing Bad Practice.
I think by "You" he means "Human". "Flame" is "religion". "Lord" is "God"