core: respect user preference on payload, smartcard and watchdog

The payload, smardcard and watchdog were copied from the instance type if it
was selected all the time. Since this properties are no longer the "marked"
ones, we need to respect the user preference on them.

Change-Id: I1bc56e7b9f6e91431acb9345b4d87e9bfe145ee9
Bug-Url: https://bugzilla.redhat.com/1149663
Signed-off-by: Tomas Jelinek <tjelinek@redhat.com>