Obviously no one has a full mental model in their head of everything going on in their phone (for example) at a given moment in time. But when it really matters, and there is a specific question to answer, and a programmer with experience writing the kind of software in question has full access to all of the source code, its possible to get an answer to why a program behaved in a particular way.
I'm a programmer, and this is what I do every day.
And in those rare cases where knowledge of the specific hardware is required, there are experts who understand the hardware and can answer the relevant questions.
So for machine learning approaches, what is the equivalent of the "source code"? What resource is there to examine to determine how the system will respond to a given set of inputs, and why? Evidently, there are not clear answers, at least for some machine learning approaches.