The Site address is a different domain that is being displayed via reverse proxy, for example:
WordPress address: http://www.cagsblog.com
Site address: http://www.ccu.edu/blogs/cags
Also, even though WP says it can't write to the .htaccess file anymore, it is still reading it. For example if I manually edit the rewrite code as it says I should in following code, all pages except the landing page return an Internal Server Error.
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /blogs/cags/
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /blogs/cags/index.php [L]
</IfModule>
The reason for the reverse proxy is because there wasn't a server or database available for me to install WP on http://www.ccu.edu so we're just making it look like it's coming from that domain.