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Regarding the whole something from nothing issue, I thought the latest ideas were that “empty” space is constantly creating and destroying matter and anti matter from “nothing”.

This is correct and his been well verified since the 1950's.

Also my only take away from the article is that scientists do not know what the universe is or where it came from.

This is not a scientific article, it is a religious article pretending to be science. That said, time -- as far as we know -- begins with the instant of the singularity. Speculation "before" that, if there is a "before" that -- is not in the realm of science. Science does not know what happens on the order of a trillionth of a second or so before the singularity, and the REALLY interesting physics happens around 10^-45 second or less.

It always seemed obvious to me that just because we can only observe this universe, that does not mean it is the “universe” meaning everything.

This is an abuse of terminology, which unfortunately some cosmologists/physicists participate in. By definition, the word "universe" means "everything that is." In correct English, if there are other realities they are still part of the "universe." If you're religious, universe is a synonym for "all of creation."

Within the region (it may be the only region there is, or not) governed by the same physical laws that we are, there are things beyond our horizon. That is, loosely, there are things within our universe we cannot see. They are moving away from us and because the speed of light is finite they are now so far away and moving so quickly that the light from them can never reach us; this is a scientifically established fact based on the expansion speed and the known start time and dimensions. So, loosely, in your language, there are already parts of our "universe" that we know are not "part" of the universe that we can know or that can even affect us...