Sorry about that, I spoke to soon. With Web Standards Advisor you are limited to running it on a local site. You should obviously not be paying any attention to the warnings about the php code as this will not be present on the live site.
One way that you might be able to use the html of your local site would be to use a tool like Site Import to import your site locally, then create a new DW site for the local copy and run the Advisor on these files. Other than this you will be running it against your source files that include the php code in them.
