I am wondering the same, @Parricull are you sure of that ?
When editing this file, for example setting short_open_tag to off and restarting apache, my phpinfo is still short_open_tag on.
Then my user php ini has not this option.
So it seems this is not the default top ini file used by the php selector version...
The php info "Configuration File (php.ini) Path" is /opt/alt/php52/usr/php, but there is no such "php" dir by default...
Does it means this dir should be created manually, copying in a default php.ini for this php version ?