To find the apache php settings try something like this.
> cd /etc/apache2
> grep -r -n -i safe_mode_exec_dir *.conf
> grep -r -n -i safe_mode.*On *.conf
If you find a gererated file, obviously you need to find the source template for it, to change what's needed there.
I just wasted a sunny Sunday on searching for where the heck safe_mode_exec_dir was changed.
And yes, Local Value in phpinfo does mean 'changed between the php.ini file and here', as you would think.
If you have an automated virtual host configuration, such as confixx, php ini values can be spread across very many files.
They can be changed in apache config files, that can have any name, but usually will end on .conf, besides in .htaccess files.