Having worked at GitHub, we used MySQL because we've always used MySQL. It works because the business depends on making it continue to work, and switching off at this point is a multi-year effort. Herculean efforts have gone into scaling MySQL, and that is not without its own issues (outages, maintenance cost, etc.).

Isolation level consistency is not a problem I heard anyone talk about, but that's probably because most devs interact with the database via Active Record which is not exactly known for its transactionality guarantees (and is, of course, a source of yet another set of problems).