If Github are building a free-as-in-free-beer tool for open source ecosystem, being a for profit company that tries to make money from proprietary software companies doesn't make sense.

If Github are a for profit company building paid tooling for paying customers who want to keep their software proprietary, then narrow mindedly designing their tooling as if everything is out in the open doesn't make sense.

Both cases show they are either naive, incompetent or in a serious misunderstanding about who their customers are.