A query action just takes your SQL and executes it. The only special behavior that's different from directly writing SQL in phpmyadmin is #__ replacement. You can't use PHP inside of SQL. To do what you're wanting you need to use a subquery or a join. Example as follows.
Code:
UPDATE `table_1` SET `column` = ( SELECT `id` FROM `table_2` WHERE `user` = '[user_id]' ) WHERE `user` = '[user_id]'
As for output it's not going to be able to output anything. You're acting on a trigger that's fired during a user update process. It's not possible to output anything during that trigger. As for the URL not working under Global please read its description carefully as it states directly it will not work unless Triggers is set to None.