Why do Python function docs include the comma after the bracket for optional args?

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The square bracket means that the contents are optional, but everything outside of square brackets is compulsory.

With your notation:

RegexObject.match(string, [pos], [endpos])

I would expect to have to write:

r.match("foo",,)

The nesting is required because if you supply the third parameter then you must also supply the second parameter even though it is an optional parameter. The following non-nested alternative would be ambiguous:

RegexObject.match(string[, pos][, endpos])

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