big difference: Keybase hosts everything, all your data is belong to Keybase. In upspin only your public key is centralized; the data can be anywhere.
Actually if you read the design document it sounds like they want you to provide some wrapper server to access, say, your photos on Google Photos through the Upspin protocol. Your photos would stay there, but authentication would be centralized on Upspin.
This was my understanding as well. Keybase goes further in that they do not have access to the file metadata either (only size, not even count - though by their own admission they could probably reverse engineer count if they tried hard).
You don't even register a single root PK with them anymore - you end up with a network of device-specifc and paper keys in their current security model. IMO, their current client is the most nontechnical-user friendly security app I've ever had the privilege to use.
Actually if you read the design document it sounds like they want you to provide some wrapper server to access, say, your photos on Google Photos through the Upspin protocol. Your photos would stay there, but authentication would be centralized on Upspin.