I don't think that naming all the pages index.php is a good idea. Best case scenario, you are loosing out on the opportunity to have keywords in the page title. Worst case scenario, the bot may say "I already indexed index.php, no need to go back there".
You might want to look at mod_rewrite if you want all your pages goind through the same script. Or you can include the script at the top of all your files
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