short answer: don't worry about it. Apple has invested heavily in CoreData and uses it extensively. wrt deleted records, Core Data will clean up its storage over time.
longer answer: to understand what's going on, you'll have to dive into the architecture and implementation of structured database systems, and specifically how SQLite (which is used by default by Core Data) organizes data and indices into its file structures. For some insights, see here https://developer.apple.com/library/archive/documentation/Cocoa/Conceptual/CoreData/PersistentStoreFeatures.html