I think what is confusing me here is Darwin's reference to Origins of Life. I understand that he is looked at as the father of the theory (though others had proposed it previously).
Well, you have to keep in mind that Darwin isn't the Theory of Evolution just as Einstein isn't the Theory of Relativity. And just like Einstein speculated about other things not necessarily related to his main work, so could Darwin speculate about issues which are not covered by the ToE.
The Theory of Evolution is by it's very nature a theory that covers the dynamics of a system (i.e. imperfect self-replicators) and not it's initial conditions (i.e. how those replicators arose). It seems that this is the point that so many creationists seem not to understand.
I understand that he is looked at as the father of the theory (though others had proposed it previously).
No, not quite. There have been other theories of evolution like that of Lamark but Darwin was the first to propose the one that is accepted today because it is supported by several independent lines of evidence.
However, he wasn't the only one who came up with this theory. Alfred Russel Wallace was a contemporary who had basically the same idea, although not as developed as Darwin's. An exchange with Wallace prompted Darwin to publish his theory sooner than he had intended.