Where does this come from?
That is how it is.
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I’m tempted to agree with StoneyB’s comment that that’s just how it is: language works that way. The repetition serves to emphasise the finality of the statement.
There is an early example of similar repetition in the Bible’s Gospel of John (John 19:22), which was originally written in Greek and translated into Latin before English:
ὃ γέγραφα, γέγραφα
Quod scripsi, scripsi.
What I have written, I have written.
It certainly has a finality in English that is presumably present in the other languages too (I haven’t studied Biblical Greek). Consequently the structure is ancient and common to many languages, not just English; and it can easily be applied to simple constructions such as “It (or that) is how it is”.