If so, the answer is that fonts are a major underpinning of how an organization or a product is presented to the world.
To make an analogy that the hn crowd might understand, the value of a typeface for a design system is like the value a cryptographic primitive or a library like openssl to a functioning security system.
Nobody (aside from designers and typographers) will think "oh wow that font is so great they must have invested a lot into it", but it underlies every written visual interaction between the brand/product/company and its audience.
That said, are there many other fonts available that fall into the appropriate style, usage, licensing terms, etc that GitHub need? Perhaps. But uniqueness is a value in itself, and having a decision about a set of fonts that the company uses is a pretty important thing.
It's like the 3 spaces or 4 spaces vs tabs discussion. Some people use one, other people use another. But in a company, having an approved typeface that is recognized internally as the typeface to use (of course, you can have different typefaces for different scenarios/uses) - is just as important as determining which one to use.