Two index.html: What are their purposes?

index.html is the page being loaded. Everyone knows what it is called, so webserver deliver it by default and native platforms via Cordova have it set as the starting point. In there the real application gets loaded via JS code. Inside the application you can do whatever you want - HomePage, LalaPage, FooPage, or something totally different. If you look into the other starters, you will see that it is not alway HomePage.