To answer my own question:
On the summary page, you have to have 'manually sync music' ticked.
But, nonsensically, on the music page, you have to have 'sync music' NOT ticked.
Then if you go to the 'on this iPhone' page, the settings and 'autofill' options will have appeared.
I still don't know why the simple seeming slider "How much free space to leave on the phone", set to 4GB, is resulting in 200MB of free space though.