Comparing the references to water in John 3:5 and 1 John 5:6: The John 3:5 reference is considered by many (and I agree) to mean physical birth, yet the 1 John 5:6 reference is considered by some to mean baptism. I believe that 1 John was written, in part, to refute false teaching and to stress that Jesus did come in the flesh. Because of that, it seems that there would be consistency in the usage of the word ‘water’ between the two passages with each one referring to physical birth. Can you point out what I’m missing?
I don’t believe that 1 John 5:6 refers to the Lord’s baptism, but to His birth. As you say, 1 John was written to refute the Gnostic error that Jesus wasn’t human. Your view that idioms tend to be consistent is also correct. In my opinion, born of water in John 3:5 and came by water in 1 John 5:6 are equivalent terms and refer to the physical birth.