Firstly, I'd like to add to the chorus saying that this is an incredible post; as a supporter of SI, it warms my heart to see it. I disagree with the conclusion - I would still encourage people to donate to SI - but if SI gets a critique this good twice a decade it should count itself lucky.

I don't think GiveWell making SI its top rated charity would be in SI's interests. In the long term, SI benefits hugely when people are turned on to the idea of efficient charity, and asking them to swallow all of the ideas behind SI's mission at the same time will put them off. If I ran GiveWell and wanted to give an endorsement to SI, I might break the rankings into multiple lists: the most prominent being VillageReach-like charities which directly do good in the near future, then perhaps a list for charities that mitigate broadly accepted and well understood existential risks (if this can be done without problems with politics), and finally a list of charities which mitigate more speculative risks.