For those who do want owin to start, <add key="owin:AutomaticAppStartup" value="false" /> won't work, but the following worked for me.
if you have a partial class "Startup" in your Startup.Auth file, create another partial Startup class in the root of your project.
define an assembly owinstartup attribute pointing to that class
create a "Configuration" method
rebuild your application
You could also create the "Configuration" method, and add the assembly attribute to the Startup.Auth, but doing it this way allows you to keep your Startup class separated by leveraging C# class definition splitting. Read more here: https://docs.microsoft.com/en-us/dotnet/csharp/programming-guide/classes-and-structs/partial-classes-and-methods
This is what my Startup.cs file looked like:
using Microsoft.Owin;
using Owin;
[assembly: OwinStartupAttribute(typeof(ProjectNameSpace.Startup))]
namespace ProjectNameSpace
{
public partial class Startup
{
public void Configuration(IAppBuilder app)
{
ConfigureAuth(app);
}
}
}