WebApplicationStarter.ConfigureApplication breaks the default routing and config on webapi

I wanted to add the project and run it as a part of my webapi project. Since it has an owin start up, I thought it would be very easy, but it it not.

The first thing you realize is that ConfigureApplication is reading from its own configuration which is private and then runs **applicationBuilder.UseWebApi(WebApplicationStarter.Configuration.Value);** which will rewrite the webapi config.

I've tried inheriting from it so I can run run another method setting it beforehand, but the class is sealed.
How are we supposed to configure it on a project consisting of other stuff?