There is an
Annotations plugin which can import annotations from the "My Clippings" file from an e-ink Kindle device into either the Comments or a custom column of a book entry in calibre.
There is nothing that handles .mbpV2 annotation files produced by the Kindle for PC/Mac apps.
There is nothing that can import or export Kindle annotations that is compatible with the way that calibre's e-book reader handles them.
Added: You can add any file type, including .mbpV2, to a calibre book entry using the method you described above, but calibre isn't going to do anything with the file except store it.