The issues you are showing in the video are not really related to the extension but the way you are using it.
First of all - the starter pages, as well as the templates are not provided by us. This is all by Adobe/Dreamweaver.
Then - using "convert to bootstrap 3" on these starter pages/templates is not right. It should only be used on bootstrap 2 pages, which you want to convert to bootstrap 3 ...
If you want the bootstrap 3 extension to properly recognize the Adobe Starter pages/Templates then, after you create these and save them go to: Commands > DMXzone Bootstrap 3 Options. There you should select local minified, and point to Main CSS File, as well as the JS File. These are the bootstrap css and js files created by Dreamweaver in your site definition - browse to and point to them:
Also - turn the automatic file update option off.
Then, when you point to the css and js files, the extension will properly recognize the bootstrap code on your page ...
Now the easier way ... create a blank new page (do not use these starter pages...), and then go to the insert panel, click the DMXzone Bootstrap 3 icon and you are done!
Now you can build the page without having to mess around the starter pages, which code is slightly modified, which of course causes issues.
So my advice is to build your bootstrap pages from scratch, applying the extension to them, and then adding the grid, elements and navigation. Also - please follow the bootstrap 3 navigation tutorials.