Hi obliat,
There are two main concerns in your question that I will to answer in details below:
<blockquote>1. There is not theme cloning or so in the tutorial.</blockquote>
Yes. We do publish this T3 documentation on how to use our ThemeMagic feature to clone a new Theme with the guide video.
<blockquote>Will template.css get overriden with template update or not?</blockquote>
Yes. The template.css and other .css files in default themes will be overwritten by updating the template. So it will be better when you take a backup before udpating the template.
But, if you create and work with the new created theme folder, the modified files in this new theme folder will not be overwritten by upading the template, because updating the template only overwrites the files in our available themes.
In addition, we want to suggest you to update the template via our JAEM component that always takes a backup of old modified site before extracting the template update. By that way, you can roll back the old site if you want.
Or You can try to use our custom.css file to protecting your modification from Compiling Less process.