1) the big advantage for developer to use this framework is the "path" correction... usually we use folders to "seperate" template and code... i'm not talking about MVC concept.. but a quick ('n dirty) approach like this is usefull to create quick project.
so instead of debuging from main site, we could concentrate on each module and combine it into one in index.php
2)Yes, i agree the solution is to remove unwanted head element manually, but i think most of WA's user are visual designer who take a lot of advantage using 'instant' (and great) solution with WA's extension... probably not many aware of this 'bug'
