1. ROWNUM 으로 정렬하시면 됩니다.
2. seq 의 역할이 있는지 모르겠네요?
 - 정렬용이라면? 같은 부모를 가진 자식끼리 값이 달라야 할텐데? 그렇지도 않고?

WITH dept_table AS
(
SELECT '00100' deptcode, '총괄부' deptname, '00000' p_deptcode, 0 seq FROM dual
UNION ALL SELECT '00003', '생산부'  , '00100', 20 FROM dual
UNION ALL SELECT '00124', '전산팀'  , '00003', 10 FROM dual
UNION ALL SELECT '00125', '생산팀'  , '00003', 10 FROM dual
UNION ALL SELECT '01028', '운영지원', '00125', 40 FROM dual
UNION ALL SELECT '00004', '인사부'  , '00100', 20 FROM dual
)
, admin_table AS
(
SELECT '00100' deptcode, 'A001' userid FROM dual
UNION ALL SELECT '00100', 'B001' FROM dual
UNION ALL SELECT '00003', 'B002' FROM dual
UNION ALL SELECT '01028', 'A002' FROM dual
UNION ALL SELECT '01028', 'C003' FROM dual
)
, user_table AS
(
SELECT 'A001' userid, 'shelley' username FROM dual
UNION ALL SELECT 'A002', 'susan'   FROM dual
UNION ALL SELECT 'B001', 'david'   FROM dual
UNION ALL SELECT 'B002', 'hann'    FROM dual
UNION ALL SELECT 'C003', 'bruce'   FROM dual
)
SELECT a.lv
     , a.deptcode
     , a.deptname
     , a.p_deptcode
     , a.seq
     , b.userid
     , c.username
  FROM (SELECT ROWNUM rn
             , LEVEL lv
             , deptcode
             , LPAD(' ', LEVEL-1, ' ') || deptname deptname
             , p_deptcode
             , seq
          FROM dept_table
         START WITH p_deptcode = '00000'
         CONNECT BY PRIOR deptcode = p_deptcode
         ORDER SIBLINGS BY deptcode
        ) a
     , admin_table b
     , user_table  c
 WHERE a.deptcode = b.deptcode(+)
   AND b.userid   = c.userid(+)
 ORDER BY a.rn, b.userid
;