That's fine when one application is using the database. I work in the enterprise space, and we have at least 5 different applications all working with the same database. Each of these applications has their own team. Expecting each team to handle constraint checking uniformly in their applications isn't always feasible, so we use foreign keys.

GitHub's approach might work fine for small, focused teams who have exclusive control over a product. However, that's not often the reality of most organizations.