Web Site Projects vs Web Application Projects

I did not notice first that there two different types of web projects namely Web Site Project and Web Application Project. When I noticed, I wonder why MS came up with two different types of projects until I read this Introduction to Web Application Projects  article. As it explains, MS created this new Web Application Project type  for those developers, who are not comfortable with certain new features such as

1. Web Site Project model creates multiples assemblies.

2. Web Site project does not use Project file.

3. Web Site Project uses new semantic like sub projects where it just meant another project which feeds its assemblies to parent's bin folder.

But essentially, it just gives additional ways to manage the web projects.