I feel it important to point out that the belief that "water" in John 3:5 means water is actually a view that has been held by virtually all Christian exegetes for the last two thousand years. Even Baptist exegetes until rather recent times agreed that the water in John 3:5 meant water and that baptism is being alluded to here, while denying baptismal regeneration; by understanding that baptism isn't the new birth itself but symbolized it.
Within the last couple months I actually did a bit of a dive into this subject by looking various commentaries of the past couple hundred years. I was curious when the "physical birth and spiritual birth" interpretation of "water and the Spirit" began to show up in commentaries. I would have to go back and look again for more details, but I was actually somewhat surprised to learn that I couldn't find commentaries from before the 1960's-70's that offered this interpretation. I simply couldn't find any commentaries, by anyone (and I specifically looked up commentaries from Baptists and others who reject baptismal regeneration) from before the mid-20th century that gave this view.
Virtually all commentaries agreed with the historic interpretation (going all the way back to the earliest commentaries/interpretations of the 2nd century) that the water in John 3:5 was water and was an allusion to baptism. Some did differ, IIRC Spurgeon understood the water of John 3:5 as being an allusion to repentance.
So whether "water and the Spirit" referred to baptism, or referred to regeneration (apart from baptism) such as understanding water as symbolic of repentance that comes with the Spirit; "water and the Spirit" were held together as a singular principle involved in regeneration. It isn't until the last half century that the two birth theory shows up anywhere. I'm still unsure, exactly, its origins; but prior to the 1960's I couldn't find anything, and by the 1980's some commentators speak of it as some kind kind of well known fact. So sometime between the 60's and 80's is likely the origin story of this particular interpretion of the text.
Also, when I did my research I didn't do anything fancy. The tools to do what I did are readily accessible by doing some Google searches.
That's how I found this:
Comprehensive Overview of the Bible Commentaries available FREELY on StudyLight.org!
I looked up information about the commentators themselves, their denomination/tradition, when they lived, etc. So anyone can look this up for themselves and see if they notice the same things I did.
-CryptoLutheran