Look! Actual ASP.NET content is back!
The documentation for WebConfigurationManager.OpenWebConfiguration says:
"Opens the Web-application configuration file as a Configuration object using the specified virtual path to allow read or write operations."
This might lead you to think you'll only find stuff from a single web.config file in the returned Configuration object - but this isn't true. The following code will return the extensions and paths mapped to the web forms PageHandlerFactory for "MyWebSite".
... and you should at least get a result of ".aspx". This ".aspx" entry probably isn't in the web.config for "MyWebSite", but it is in the machine level web.config file (found in %Windows%\Microsoft.NET\Framework\v2.0.50727\CONFIG) by default.
Remember .NET configuration files are hierarchical, and if you look at the documentation for System.Configuration you'll find (emphasis mine):
The Configuration class instance represents the merged view of the configuration settings that apply to a specific physical entity, such as a computer, or to a logical entity, such as an application, or a Web site.