Arrgh. Newbie mistake. I needed to replace 'phone_office' with 'id' within the SELECT statement. This should be the syntax:
'phone_office' => array(
'query_type'=>'default',
'operator' => 'subquery',
'subquery' => array(
'SELECT id FROM accounts WHERE phone_office LIKE "%"',
'SELECT id FROM accounts WHERE REPLACE( REPLACE( REPLACE( REPLACE( REPLACE( phone_office, "+", "" ) , "-", "" ) , "(", "" ) , ")", "" ) , " ", "" ) LIKE "%"',
'OR' =>true
),
'db_field'=>array('phone_office'),
'vname' =>'LBL_PHONE_OFFICE',
),
Now it works as it should. I guess I found out today that just because it works on MySQL doesn't necessarily mean it's gonna work in SugarCRM. Thanks for helping me out!