You may be confusing things here. You have code to add variables, then you're applying configuration and then you're attempting to add another variable. Ignoring the configuration steps for now, you should be adding a variable to your package called OutputFolder in the Template namespace.
The problem is that you are attempting to assign the value of this variable to be "FolderRoot's value concatenated with \Output\" That will be evaluated when the code is executed which results in what you are seeing as \Output.
Using the method and link provided by billinkc, I was able to have BIDS generate a variable value successfully using the following code.
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