I think this is a relatively new usage. At least, I don't remember hearing it until just a few years ago.
For example, someone might say that the New York Times is a newspaper based out of New York. Really? So where is it actually based? Indianapolis? No, it's not based out of New York, it's based in New York.
I suppose the idea is that it operates all over and isn't limited to New York. But based in doesn't imply anything of the sort. We might as well stop saying that the capital of the United States is Washington, DC and instead say that the U.S. government is based out of Washington.
And now I must leave the house out of which I'm based and go driving all over the damned place to do the Saturday shopping.