This is an example of the XOR swap algorithm:
https://en.wikipedia.org/wiki/XOR_swap_algorithm

Another method of getting the result you want is to use CROSS APPLY with TOP(1)::
;WITH CTE AS (select distinct Id from CustomerSourceDE)
SELECT T.* FROM CTE
CROSS...

Sounds like you need to create some dynamic SQL.
There are a few articles on this:
https://www.mssqltips.com/sqlservertip/2783/script-to-create-dynamic-pivot-queries-in-sql-server/
https://stackoverflow.com/questions/10404348/sql-server-dynamic-pivot-query
https://social.technet.microsoft.com/wiki/contents/articles/39000.sql-script-convert-rows-to-columns-using-dynamic-pivot-in-sql-server.aspx

Rows per batch should be set to the total number of rows on the table.
Set the table lock checkbox on the staging table
Set the maximum insert commit size...

You can create a DOS batch file that calls the .vbs file with cscript command
https://ss64.com/vb/cscript.html

I just tried your query with 0.5 million in MyTable and 30 million in MyAudit. And it ran in 8 seconds on my work desktop. Maybe you need better hardware?

SELECT a.SQLInstance,
   a.DBName,
   Max(a.SvcStartDate) as MaxSvcStartDate,
   Sum(a.DaysUpTime) as SumDaysUptime
FROM #tbla a
WHERE NOT EXISTS(SELECT *
      FROM #tbla b
      WHERE b.Used=1...

I suspect you need an index on one of the tables to improve the query performance.
You really need to work out which queries within the set of queries is...

Another way of writing the query:
;WITH DS AS
(
  SELECT DISTINCT
       DS.DateKey,
       DS.SafeRegionKey,
       DS.Attribute3ValueKey
  FROM rstore.OutputDataset...

Another way of doing it:
;with myTable AS
(
SELECT *
FROM (
VALUES (1,'B-6916','SEOK'),
(2,'B-6916','SEOK'),
(3,'B-6916','SEOK'),
(4,'B-6916','SEOK'),
(5,'B-6916','SEOK'),
(6,'B-6916','SEOK'),
(7,'B-6916','NEOK'),
(8,'B-6916','NEOK'),
(9,'B-6916','SEOK'),
(10,'B-6916','SEOK'),
(11,'B-6916','SEOK')
) V(ID,...