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At a high level, I think if you pass the filename/path into a Dynamic Input tool, you should be able to properly read the file at runtime, as Alteryx can natively read from Zip files. Unfortunately, I don't have a great example of this, as I don't use Qualtrics, so this is just a theory for now.
Thanks @Jdang1. I was struggling with the responseexports query from Qualtrics with the Content-Type. It works now thanks to your workflow.
I am also able to read the zip file with the dynamic Input tool:
Create a text field containing the Qualtrics output file - however keep a .tmp extension (or something else) because for an unknown reason you can't open the zip file if you chose a .zip file extension in your output file
Create another text field containing the Qualtrics output file and the name of the file you want to unzip in the Qualtrics zip archive (e.g., "C:\Temp\test.tmp|TEST.csv")
Specify the name of the Qualtrics output file in the Download tool instead of using a temporary file
Use the Dynamic Input tool with your field name created in step 2