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It really depends on how the structure of the company is setup. If they're just a division, they're not really a CEO; but if all Microsoft did is buy up all the shares of Github, and otherwise left them alone, they really ARE the CEO.

Until the shareholder decides to tell the board to fire him.

Major subsidiaries within a large company can and do have separate CEOs. For example, YouTube also has a separate CEO (previously Susan Wojcicki, and now Neal Mohan) under Sundar Pichai.

It’s also common within Microsoft. I can’t speak to when/why they decide to do it, but the leads for the Microsoft Gaming (Phill Spencer) and LinkedIn [acquired 2016] (Ryan Roslansky) are both CEOs in the org chart at Microsoft.

What is a CEO if not a high level manager?

All CEOs are managers, but not all managers are CEOs. A CEO is the highest ranking executive.