Using php command to pass custom php.ini values into drush phar
You did it exactly right -- just add the additional Drush command, options and arguments after the part you already typed in.  For example:

php -d memory_limit=256M /usr/local/bin/drush --php-options=memory_limit=256M --root=/path --uri=example.com status

That's kind of a lot of typing, so you might want to make an alias:

alias drush='php -d memory_limit=256M /usr/local/bin/drush --php-options=memory_limit=256M'

Then:

drush --root=/path --uri=example.com status