Answer one I have not yet created a plugin to enable native Joomla! searches. I would like to do that in the future, but it will take some learning on my part before I can accomplish that.
Answer two Thus far I only allowed plugins in the individual word view and not the category or word list views. You are right though, it would be nice for the words to be linkable in the list views also. The reason I have not enabled them in list views is because I did not want other plugins, like hmtube, to display in the list. Maybe I can selectively allow only the gnosis plugin and the others. I'll see what I can figure out =)