Granted I'm not a software developer, so the things I work on tend to be simpler. But the people I know who are recognized for "knowing how the whole thing works" are likely to have earned that distinction, not necessarily by actually knowing how it works but:

1. The ability and interest to investigate things and find out how they work, when needed or desired. They are interested in how things work. They are probably competent in things that are "glue" in their disciplines, such as math and physics in my case.

2. The ability to improvise an answer when needed, by interpolating across gaps in knowledge, well enough to get past whatever problem is being solved. And to decide when something doesn't need to be understood.

> Granted I'm not a software developer, so the things I work on tend to be simpler.

Intriguing statement. I've worked in a number of disciplines over the years and software, by far, presents the simplest things of all.