I've been wondering this myself. I think the update function from the GUI use the FreeNAS iocage repository to update when you have a jail that was created through the installation of a plugin. I've recently moved entirely from the plugins to manual installed jails and then install the applications myself using the most current version of the FreeBSD repository.
Another finding I had when using the update function from the GUI packges I installed manually weren't there anymore. I had a plugin jail in which I installed nano. After using the GUI update function it was gone.
Wonder what the actual answer is to this question.