You cannot redirect an index file to the root. The Web server will crash with too many redirects.
Any file named "index.html", "index.htm", "index,shtm", "index.shtm", "index.php", or "index.asp" will generally be served if the directory name is requested (this is always set up in the Web server configuration but most default installations handle these file extensions).
There is no redirection involved. If you link to or request "example.com/index.php" that URL will be honored by the Web server. A search engine may treat it as separate and distinct from "example.com" because there is a hierarchy of preferences among the file extensions and the search engines have no way of knowing whether a site is serving content on two or more of these file types.