Are you aware that you'll get 2 result sets when @opMode is NULL?

Can you post DDL and sample data for FunctionPermission table? The problem might be related to it and the FOR XML.

I wonder if the OP was able to use a version still under mainstream support and used the sequence to solve his problem. Or maybe the previous option was kept...

Additional to what Steve just mentioned. You should also take into account that there's additional time when you run the SSIS from your machine as the data needs to travel...

For UPDATE vs MERGE, I would choose UPDATE hands down. For an upsert, I would have to test again but I have encountered problems.
https://www.sqlservercentral.com/Forums/1615384/Long-running-MERGE

Not really a suggestion because the solution posted by DesNorton should be better but I just wanted to have some fun.

SELECT * ,
  STUFF((...

This would add the nulls row only if there's not a row in the table.

SELECT id,
   name,
   createdDate
FROM @sample
RIGHT JOIN (SELECT...

https://docs.microsoft.com/en-us/sql/t-sql/statements/alter-table-transact-sql?view=sql-server-2017#syntax

Here are some pages where you can read about Sequences:
 https://docs.microsoft.com/en-us/sql/relational-databases/sequence-numbers/sequence-numbers?view=sql-server-2017
 https://www.red-gate.com/simple-talk/sql/learn-sql-server/sql-server-sequence-basics/
 http://www.tech-recipes.com/rx/60072/beginners-guide-sequence-objects-sql-server/