If my build system has already encoded all of my dependencies in a secondary layer (my build files), do I care about any of these concerns? 

Or, put another way: is the current debate about "I want the build to be synthesized at compile-invocation time from source, without that secondary layer"? 

I'm reasonably sure from past experience is that a proper modular and parallized build requires that secondary layer. (To say nothing of performance concerns: rescanning constantly is a waste of computation.)

Or am I misunderstanding?