Talking about the games original files not new moded ones.

Not that I will actually delete the BSA (well I might) but just for my clarification, will the game only use the data unpacked from the bsa, or would it ignore what is unpacked and use the bsa anyway?

Files in a BSA will be overridden by files outside of a BSA, I believe. Texture replacers without data files would have to rely on that.

Cipscis

Unless the BSA is loaded by a plugin (the vanilla ones aren't), loose files will overwrite BSAs.