I think we're looking at overall performance including future expansion. We know we want a server dedicated for just .NET applications (That would be the application server) but it was the Web Server and Web Services that has us confused. I'm used to, personally, having it where I had a web server (Apache) and I hosted everything there all on the same machine. Now if they are thinking programs like SharePoint is a Web Service I get that but, in that model, would Application Center control it?
Life was much easier as Linux but now M$ has taken over.