If you have an API, the API determines what you are and aren't allowed to do. It can also do input validation, deal with referential integrity.
Encapculation via an API also means you can change the internals without impacting the API. You could even swap out the SQL backend by something completely different, and Enigma and plugins would be none the wiser. So the code is loosy coupled of even completely decoupled. If you access the SQL DB directly, you haven't improved anything compared to the current situation. You can still incorrectly modify the data, and if something in Enigma changes, all plugins break. Tight coupling is evil.
So it is about stability, compatibility, and extensibility. API's should be documented, and have a known input and output. Encapsulated code can be tested in isolated, and tested code is stable code. Code changes can be tested without having to test the API, as that is tested seperately and known to work. It also greatly reduces regression errors.
Something every developer should welcome. And don't forget the users, they will get a much better and more stable and profesionally build product.
So it has nothing to do with intelligence, these are completely normal and standard development practices.
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