Please could anyone explain the concern about keeping arriving and departing passengers separated?
Before all the changes in security, if incoming and outbound were not separated, there was the possibility, (and still could be) of a passenger bringing something with them from a less well regulated airport (internal flights were almost like bus services, with minimal formalities) and passing "something" to an outbound passenger. I leave to your imagination what "something" could be, and terrorism is not the only possibility here.
In theory, it's less of a risk now, but there are still regional airports that have very little in the way of scanning and the like, so the risk is there. In some cases incoming transit passengers now have to pass through security scans before getting to the "gate" area, so that problem is now resolved.