You are correct, there is an extra copy stored on your machine when using 'Connect to iTunes'. This is due to the architecture of calibre's database.
If you'd rather avoid the extra copy being stored, you can install the
Apple iDevice driver instead of connecting to iTunes. The principal difference is that books are sent directly to iBooks on the connected iDevice, and a copy is not saved in iTunes. iTunes is still utilized to manage books on the connected iDevice.
See the post #2 in the forum sticky '
Calibre + Apple iDevices: Start here' for an in-depth explanation of how and where books are stored when sent to iTunes using 'Connect to iTunes'.
G