Why would I not be able to make inferences about the software the servers are running if the chances on lying on the letter is low? I haven't read Signal's source code, and yet I believe with just as much confidence that they aren't logging extra information as if keybase had sent the same NSA letter. To me, Signal's source code is effectively closed, and reading it wouldn't increase my belief. (Have you read all of their server's source code? If not, why do you justify your belief?)

The article on attested contact discovery states "Of course, what if that’s not the source code that’s actually running? After all, we could surreptitiously modify the service to log users’ contact discovery requests. Even if we have no motive to do that, someone who hacks the Signal service could potentially modify the code so that it logs user contact discovery requests, or (although unlikely given present law) some government agency could show up and require us to change the service so that it logs contact discovery requests.", which is exactly the point I'm making. They choose to solve it by signing code and ensuring that exactly that code is running (seems like they just move the trust to Intel. Hopefully SGX never has any bugs like https://github.com/lsds/spectre-attack-sgx or issues with the firmware, as noted by the Intel SGX security model document), which is fine, but an equally valid way to do this is to make it so that the secure operation of the system does not depend on what code the server is running.

Doing that has some tradeoffs: there's usually overhead with cryptography, or an algorithm you need may not even be possible (Signal disliked those tradeoffs for this specific algorithm), but for some algorithms, it's entirely possible to do. For example, one can audit OpenSSL's code base, and determine, regardless of what the middle boxes or routers do, that the entire system is secure. Just replace OpenSSL with keybase's client, and middle boxes with keybase's servers, and do the auditing. Hence, open sourcing the server is not necessary for security. Would it be great if more systems could be audited? Absolutely. Is it always necessary for security? Absolutely not.

edit: Another quote from the article: "Since the enclave attests to the software that’s running remotely, and since the remote server and OS have no visibility into the enclave, the service learns nothing about the contents of the client request. It’s almost as if the client is executing the query locally on the client device." Indeed, open sourcing the code running in the secure enclave is effectively open sourcing more code in the client.