I tried to install my site's root folder outside public_html, because its an addon domain and I didn't like the idea of having maindomain.com/addondomain.com/ and this caused the mod_rewrite warning to appear during installation. I ignored it and installed, but my site had the index.php problem, suc as addondomain.com/index.php/contact-us
I found a solution by copying the .htaccess file from the maindomain.com root folder (which already had an SS installation) to the root folder of the addon domain
For reference, .htaccess contains the following code:
### SILVERSTRIPE START ###
<Files *.ss>
Order deny,allow
Deny from all
Allow from 127.0.0.1
</Files>
<Files web.config>
Order deny,allow
Deny from all
</Files>
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteCond %{REQUEST_URI} ^(.*)$
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule .* sapphire/main.php?url=%1&%{QUERY_STRING} [L]
</IfModule>
### SILVERSTRIPE END ###
and now the site works perfectly (hopefully no future problems)
I thought this might help
Regards
Ali