"split the difference"  Now your thinking like me. 😀

At my prior job we used 3 part naming, our database names were the same on DEv, TEST, QA, PROD.  My current job the database names start with the prefix...

I don't have a solution, but I'm curious as to how to get the desired results.  I don't think Jonathan will work with different data.
I modified the data and...

Without data to test with not sure if this would work, here is what I would try:
DECLARE @startdate AS DATE;
SET @startdate = '2016-01-01';

WITH EncounterProc_CTE...

If you are wanting to be able to write out 2 different formats to the same file, you will need to create 2 different 'layout' connections in your connection manager.

I'm assuming what you mean is you want to be ale to 'append' the data from the second data flow task to the data from another data flow task.

A couple things I'd like to see are the ability to link multiple email accounts.  I liked the change from the prior version, looking forward to the new version.

To paraphrase your quote Eric, "The SSIS universe is complicated, but your SSIS life is only as complicated as you choose it to be."  
I choose an uncomplicated SSIS life.