These settings are made for specific sessions, I guess. So start Kate, choose "new session" and configure the window's layout. Also do not forget to check "Save Window Configuration". Then hide the filesystem browser and and the document list. There is also an option to hide the navigation bar (alt+ctrl+shift+f). Now quit Kate. If you restart Kate now and choose "new session", the filesystem browser and the document list should be hidden.
At least, this worked for me. Opening any other session should result in filesystem browser and document list _not_ being hidden. I did not find a global setting for this, so I guess you have to configure every session this way.
I hope this works for you.