This doesn't actually seem extravagant: Assuming they bought (or rented), rather than built, their office, they probably just had a bunch of extra space. Even if they didn't, only a company expecting growth to completely die would build an office with only as many rooms as necessary for the company at that moment in time.

What's more efficient than empty rooms? Giving departments a bunch of rooms to do cool stuff with. The expected return on pretty much anything at GitHub's scale is higher than the cost of stocking a room full of equipment.