The JavaScript contained within a Twine generated story HTML file falls into one of two categories:
1. That which was added by the Author to their project's Story Javascript area.
This JavaScript is embedded into the #store-area element of the selected Story Format's template as is, there is NO minification process being applied to this code by the Twine application. The same is true for any CSS placed within the Story Stylesheet area.
eg. If the code within the Story Javascript area is formated, has blank lines, and includes comments then the copy of it within the #store-area element will also have them.
2. That which makes up the story format's built-in JavaScript based engine.
Each Story Format Developer is responsible for suppling it's template, they also control if the CSS and JavaScript that comes with the template has been minimised or not. The Developers often include copies of third-party JavaScript libraries (like jQuery) in the template, these are often pre-minimised.
If you want a unminimised version of a particular Story Format then you may have to build your own custom copy of it. Each Story Format has it's own repository.
note: The tweecode/twine repository you linked to is actually the one for the discontinued Python based Twine 1.x application. The HTML5/Electon based Twine 2.x application's repository can be found here.