Stackoverflow is switching to use system font https://news.ycombinator.com/item?id=27063991 Other big site such as Github is using system font as well. It appears there is a trend to abandon web fonts.
In that StackExchange post you linked to, they mentioned make their own branded web font. That's definitely what I would be advocating for if I were there. The case for Github making their own font is even stronger. Microsoft has a very good font team. Designing a family of brand fonts for GitHub would be a very cool project (How many brands care about their fixed width font as much as github?)