I've not tested setting it in the .htaccess file using php_value but I don't see how that is even relevant nor can I imagine why that should give different results.
With it set to ON in the php.ini file (and showing up as such in phpinfo()), it does not work with LSAPI 5.2. It works as intended with LSAPI 4.10.
register_long_arrays is set to be removed in PHP 6. That's quite a ways off for most (shared) hosting environments where this setting can actually be a concern.