If I remember well (cause I've looked all the morning thru the books,and I couldn't find it) the sensing will be right provided that you set the ILS course on the MCP course window,not the track course (backcourse) that you are flying.After engaging on ils,the FD bars will not receive commands from the FMS.
But again,I maybe wrong.I'll check my books,I know I've read about this somewhere.