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Index.php (or .html in some cases) is the default page ANY domain will look for.
For example, if you go to http://www.cnn.com , you’re actually looking at http://www.cnn.com/index.html , go ahead and try it! Adding in “index.whatever” to your URL is redundant, but it won’t hurt anyone
Magento is really not ideal from the point of view of SEO. Very many obvious functions are implemented not quite right.. As a variant, you can try the ready extensions. For example, I use this one http://mirasvit.com/magento-extensions/advanced-seo-suite.html and very satisfied with results. There are a lot of similar extensions.