[itimpi]

No - the author/title are not normally taken from the book title, but from the metadata stored inside the book. They are only taken from the filename for formats that do not support metadata (e.g. text files), and this occurs at the time they are imported and the results are stored in metadata.db. After that Calibre does not refer to the underlying files containing the actual books except for exporting or copying to a device.

As to whether alternative naming will be possible in the future, Kovid has state that this is on the TODO list, but unlikely to appear anytime soon as it is a lot of effort to change.