I think his observation is relevant at any level of abstraction. Gates had a complete sense in his head of how his program worked at the level of machine langu

I think his observation is relevant at any level of abstraction. Gates had a complete sense in his head of how his program worked at the level of machine language. But not at a lower level of CPU microcode, or transistors. So even he, even then, was not claiming to have "total" understanding in the sense I think you mean. Likewise if the Linux kernel (or your distributed web app) is organized into a reasonable set of "chunks", then it is possible to have usefully complete sense of how it works. The implication being that if it's not organized -- or organizable -- like that, you have a problem.