SQL Server: How to add a full join to two tables but have matches line up?
You can use a FULL OUTER JOIN.

SELECT ISNULL(a.item_id, w.item_id) AS item_id,
    a.alternate_code_ERP, w.web_alternate_code
FROM alt_code_erp a
FULL OUTER JOIN web_alt_code w
    ON a.item_id = w.item_id
    AND a.alternate_code_ERP = w.web_alternate_code
ORDER BY 1, ISNULL(a.alternate_code_ERP, w.web_alternate_code)


I added an ORDER BY in case you need it.  It's still not exactly the same but without doing some string manipulation you aren't going to get an order of item_id like you want.