My previous question was marked as duplicate and linked to a question that was too general and whose answers were scattered and unfocused.
I'm not asking about development time or runtime speed or memory footprint.
Is there ANY difference in API or OS access between NDK and Java?
Yes, there is a huge difference. There are quite a lot of things you cannot do in NDK directly, and you must call Java methods that will invoke OS API. There are also APIs that are available only in NDK, but the NDK is much more limited. You can see a brief summary here: Android NDK Native APIs.
BUT - why are you addressing this in a general manner? You should be examining you specific need, your system requirements, and see if you can benefit from using the NDK.