You have to look deeper into GitHub's intended audience. GitHub was built by developers for developers, a majority of whom use the repository to store their code for software development projects that they're working on. I would assume a majority of GiHub's user base are of the technical breed, in which case we would consider them "advanced" users.
GitHub is more of a utility/hosting app, with a few things that may need more prominence than others such as creating a pull request (i.e. the bright green button). Each user comes in and may need to do different things, so it is likely a choice by the designer's at GitHub to not put too much emphasis on any specific items. Any elements that do have emphasis on them are likely used more based on usage stats.
For example, on the screenshot you posted, the most apparent elements are the Language Statistics and the green, "Compare, Review or Create Pull Request" button. In this case, the language stats (amongst other things) provides the user a quick overview of how much dev work was put into it via the languages used and the Pull Request button is there for when the user needs it. Based on usage, the designers/devs likely learned that this feature was used more at this point in the workflow.
In terms of call to action, think about how designer's or photographers use Photoshop, it's a tool. There may not be an intended flow or CTA per se, it's just a "toolbox" with all the tools you need to get your job done. The different ways of using it varies user by user.