Its very much like an experienced coder going into established codebases and being able to more quickly make changes and improvements. No codebase is perfect and they all seem to have their own uniqueness just like no house is perfect and all have their own quirks. How good or bad it is can be determined by the experience and foresight of the person doing the work but there will still always be uniqueness and quirks.
Once I finally internalized it, I really appreciated the history of my home and the things people did to solve problems as time went on just like a mature codebase. I would argue as long as the property is generally good, its just a fact of life to have to deal with the rest.
That's not to say a good inspector will find every fault either. They don't tear walls open, and they don't have x-ray vision. They only inspect what they can see.