'Prepare image for capture' will get the installed agent ready for imaging (gets rid of GUID, etc), sysprep the image, and reboot to automation/pxe for you. It's actually the preferred method of imaging and it works really well (There's a sticky post about it in the DS forum). The custom unattend file only comes into play on the deploy side via injection by the deploy image job, so your custom unattend will work normally if you specified it in your deploy job.