GROUP_CONCATを入力としてSELECTWHEREIN

このソリューションには熱心ではありませんが、実行可能です：-

SELECT a.ID, 
        a.country, 
        a.region, 
        a.item
FROM whitelist a
INNER JOIN 
(
    SELECT group_concat(ID) AS ID, USERNAME, COMPNAME, PUBLISHER, NAME, VERSION, COUNT(*) AS AMOUNT
    FROM software_checklist
    GROUP BY USERNAME, COMPNAME, PUBLISHER, NAME, VERSION 
    HAVING AMOUNT > 1
) tmp
ON FIND_IN_SET(a.ID, tmp.ID)