About index.php being shown I remember reading several other posts where you tell people to make sure that mod_rewrite is activated on the server for this to not happen. I checked my phpinfo.php file and this mod was not listed, so I contacted my host and they told me that it is indeed activated as it is needed for CPanel, but they hide it so users do not mess with the setting.
So all in all I don’t know either why index.php is showing up in the URL, it’s been there on all installs I’ve done so far (I reinstalled a few times to try to fix some glitches). I used Softaculous installer, if that changes anything.