When you export a sequence, the ‘export quicktime move’ uses the settings of your sequence. So however your sequence is set up thats what it exports. The self contained option is simply making a true contained quicktime with all the media within the file. If the box is unchecked, then its simply a reference quicktime and will not work unless the original media is on your local drive or connected network drive(s).
The quicktime conversion option gives you the full range to export whatever you need. If your sequence is pro res and you need a H264 QT then thats where you would go.