I do however believe I understand where there may be some additional confusion, and this relates to the 2 changes cPanel version 66 did make to topics related to what's been discussed in this ticket:
1) First change - WHM -> MultiPHP INI Editor now writes to /opt/cpanel/ea-phpXX/root/etc/php.ini instead of ../php.d/local.ini (since local.ini's existence essentially makes user's php.ini files useless under suPHP since local.ini overrides everything within it).
2) Second change - cPanel -> MultiPHP INI Editor now edits .htaccess, .user.ini, OR php.ini, depending on your handler. In cPanel v64, this interface would simultaneously edit php.ini, .htaccess, and .user.ini.
Due to the way local php.ini files work under suPHP (in that they *replace* system-wide php.ini), this file only containing a few directives means all other PHP options will be PHP defaults. This behavior was present in both 64 and 66. I've verified this by installing cPanel 64.0.36 to a test environment and testing further.
The difference between 64 and 66 however is that the local.ini has been transferred over to the system php.ini, leaving the incomplete php.ini files in user directories to result in all their un-speecified directives to be PHP Defaults. I'll agree that this may seem confusing, as the cPanel PHP INI Editor is in the context of making changes to specific directives, when in reality, submitting that form creates a php.ini file which ultimately sets most PHP settings to PHP defaults.
So, in summation, we have below the differences between cPanel 64 and 66:
v64: User's MultiPHP INI Editor in cPanel would write to php.ini, .user.ini, and .htaccess. Under suPHP, the php.ini would override the system-wide php.ini. The presence of a local.ini in /opt/cpanel/ea-phpXX/root/etc/php.d/ would override all the user's php.ini settings, but their customizations were re-implemented with the .user.ini file that was also present.
v66: User's MultiPHP INI Editor in cPanel writes to php.ini for suPHP, .htaccess if they're using DSO, and .user.ini if they're using CGI or PHP-FPM. Due to the lack of local.ini, any settings not specified in their local php.ini would be PHP defaults, leaving ONLY the user's customizations, and no server-wide configurations.