Kenneth's suggestion wont work as stated in the comments.
However you can write your own implementation of IHttpControllerSelector and only assign it when you map the api routes. I used the implementation in this article as a base and modified it.
Then its just the small issue of replacing the default selector after mapping the route in WebApiConfig like this (where CustomControllerSelector is my implementation):
public static void Register(HttpConfiguration configuration)
{
var apiRoute = configuration.Routes.MapHttpRoute(
name: "API Default",
routeTemplate: "api/{controller}/{id}",
defaults: new { id = RouteParameter.Optional, controllerNamespace = "api" }
);
configuration.Services.Replace(typeof(IHttpControllerSelector), new CustomControllerSelector(configuration));
}