The problem is I don't think that possibility can be evoked for situations where one discovers more and more things are part of a single, vast, interrelated system.

At least until we get "AI Complete" approach, we can't expect to suddenly a means to "debug" a system crudely analogous to a "million lines of spaghetti code" (and yes, only crudely analogous but the ways that analogy break down only makes the whole thing harder to understand).