They're "complex thingamabobs" because our applications are. Which is exactly why we want to wrap them up and isolate them and expose as narrow interfaces as possible.

Containers are a symptom of our still immature ways of building applications.

The problems you bring up would still be there without containers, but you might not notice them, until you e.g. want to bring your setup over to another machine, for example.

Or want to duplicate it somewhere else. Or want to upgrade something else on you machine that just happens to interact badly with your setup.