I can't account for why the wizard assigns php virtual to your page, perhaps its a new thing - maybe Jason can help with that. 
That's a Dreamweaver site setting.
When setting up the site, there is an option to Create Links relative to:
Site / Document
If you use Site, Dreamweaver uses the virtual() function for including files, if you select document it uses the require_once() function.
I noticed that there's a '_notes' folder that was generated
Also Dreamweaver. The _notes folder is created by Dreamweaver. it does not have anything to do with the webassist extensions.
In the Site settings, there is a section for Design Notes, if you save design notes, they are stored to the notes folder.
Go to File -> Design Notes to enter notes for a page.
