1) Please run this script and read my comments.
2) I hope this answer will help you.
3) The precision for SUM()-SUM() is 2 because you choose first to sum(SUM(total) and SUM(rem)) and then to subtract (SUM(total) - SUM(rem)).
4) My advise is to use SELECT t.code, SUM(t.total - t.rem) AS diff ... (first subtract and then SUM).
5) You may read my answer to this question SQL Numeric data type truncating value?: 
DECLARE @Test TABLE(
    code  varchar(15),
    total numeric(13,2),
    rem   numeric(13,4)
);
INSERT  @Test (code, total, rem)
VALUES  ('001', 11.78, 5.6789);
--Test [1]
SELECT  dt.*,
        SQL_VARIANT_PROPERTY(dt.diff, 'BaseType') AS diff_BaseType,
        SQL_VARIANT_PROPERTY(dt.diff, 'Precision') AS diff_Precision,
        SQL_VARIANT_PROPERTY(dt.diff, 'Scale') AS diff_Scale
FROM
(
        SELECT  t.code, t.total - t.rem AS diff
        FROM    @Test t
) dt;
/*
Operation: e1 - e2
Result precision: max(s1, s2) + max(p1-s1, p2-s2) + 1 = max(2,4) + max(13-2, 13-4) + 1 = 4 + 11 + 1 = 16
Result scale: max(s1, s2) = max(2, 4) = 4
*/
--Test [2]
SELECT  dt.*,
        SQL_VARIANT_PROPERTY(dt.diff, 'BaseType') AS diff_BaseType,
        SQL_VARIANT_PROPERTY(dt.diff, 'Precision') AS diff_Precision,
        SQL_VARIANT_PROPERTY(dt.diff, 'Scale') AS diff_Scale
FROM
(
        SELECT  t.code, SUM(t.total - t.rem) AS diff
        FROM    @Test t
        GROUP BY t.code
) dt;
/*
Operation: SUM(e1 - e2)
Result precision: 38--For SUM function, I think (it's just a hipotese), SQL Server choose the maximum precision to prevent the overflow error
                    Argument:
                    DECLARE @t TABLE (Col NUMERIC(2,1)); INSERT @t VALUES (1);
                    SELECT  SQL_VARIANT_PROPERTY(SUM(t.Col), 'Precision') FROM @t t;
                    Result: precision = 38 (maximum DECIMAL/NUMERIC precision)
Result scale: the same scale as (e1-e2)= 4 (please see Test [1])
*/
--Test [3]
SELECT  dt.*,
        SQL_VARIANT_PROPERTY(dt.SUM_total, 'BaseType')  AS SUM_total_BaseType,
        SQL_VARIANT_PROPERTY(dt.SUM_total, 'Precision') AS SUM_total_Precision,
        SQL_VARIANT_PROPERTY(dt.SUM_total, 'Scale')     AS SUM_total_Scale,
        SQL_VARIANT_PROPERTY(dt.SUM_rem, 'BaseType')    AS SUM_rem_BaseType,
        SQL_VARIANT_PROPERTY(dt.SUM_rem, 'Precision')   AS SUM_rem_Precision,
        SQL_VARIANT_PROPERTY(dt.SUM_rem, 'Scale')       AS SUM_rem_Scale,
        SQL_VARIANT_PROPERTY(dt.diff, 'BaseType')       AS diff_BaseType,
        SQL_VARIANT_PROPERTY(dt.diff, 'Precision')      AS diff_Precision,
        SQL_VARIANT_PROPERTY(dt.diff, 'Scale')          AS diff_Scale
FROM
(
        SELECT  t.code, 
                SUM(t.total) AS SUM_total, SUM(t.rem) AS SUM_rem, SUM(t.total) - SUM(t.rem) AS diff
        FROM    @Test t
        GROUP BY t.code
) dt;
/*
Operation: SUM(total) (<> e1 + e2 + ...)
Result precision: 38--I think SQL Server choose the maximum precision to prevent the overflow error
Result scale: the same precision as total= 2
*/
/*
Operation: SUM(rem) (<> e1 + e2 + ...)
Result precision: 38--I think SQL Server choose the maximum precision to prevent the overflow error
Result scale: the same precision as rem= 4
*/
/*
Operation: SUM(total) - SUM(rem) = e1 - e2
Result precision: max(s1, s2) + max(p1-s1, p2-s2) + 1 = max(2,4) + max(38-2, 38-4) + 1 = 4 + 36 + 1 = 41 
but max. precision is 38 so result precision = 38
Calculated result scale: max(s1, s2) = 4 
but because the real precision for result (41) is greater than maximum precision (38)
SQL Server choose to decrease the precision of the result to 2 (please see Test [3] - diff_Scale).
In this case (the real precision for result is greater than maximum precision) I think the 
expression for result's precision is max(s1, s2) - (real precision - maximum precision) + 1 = 4 - (41 - 38) + 1 = 4 - 3 + 1 = 2
For example you could try to modify the definition of total column to `total numeric(13,1)` 
and you will see that the precision for SUM(total) - SUM(rem) becomes 4 - 4(4+37+1=42) + 1 = 1
*/
Results:
--Test [1] SELECT t.code, t.total - t.rem AS diff
code diff   diff_BaseType  diff_Precision diff_Scale
---- ------ -------------- -------------- ----------
001  6.1011 numeric        16             4
--Test [2] SELECT t.code, SUM(t.total - t.rem) AS diff
code diff   diff_BaseType diff_Precision diff_Scale
---- ------ ------------- -------------- ----------
001  6.1011 numeric       38             4
--Test [3] SELECT t.code, ..., SUM(t.total) - SUM(t.rem) AS diff
code SUM_total SUM_rem diff SUM_total_BaseType SUM_total_Precision SUM_total_Scale SUM_rem_BaseType SUM_rem_Precision SUM_rem_Scale diff_BaseType diff_Precision diff_Scale
---- --------- ------- ---- ------------------ ------------------- --------------- ---------------- ------------------------------- ------------- -------------- ----------
001  11.78     5.6789  6.10 numeric            38                  2               numeric          38                4             numeric       38             2