I get what you are saying and it is definitely true, that systems can become too big to keep in mind completely. However, with proper and non-leaky abstractions it should be possible to reason about the system at each level of abstraction, without having to think about the lower level. The thing is then, that one could descend into the level 1 lower than one is looking at, if needed, and find out, that a simpler primitive could be used to cover more ground.
For example: Exceptions can be implemented using continuations. A return statement can also be implemented using continuations. Both can be implemented using the same concept. On the layer of exceptions and return statements, they seem like different things, but we can look under the hood and see, that we could use continuations, a single concept, to express both, if we wanted. With such optimizations one can reduce the number of concepts on needs to keep in mind lower and the system more understandable.
For example: Exceptions can be implemented using continuations. A return statement can also be implemented using continuations. Both can be implemented using the same concept. On the layer of exceptions and return statements, they seem like different things, but we can look under the hood and see, that we could use continuations, a single concept, to express both, if we wanted. With such optimizations one can reduce the number of concepts on needs to keep in mind lower and the system more understandable.