I think you're taking my comments a little too specifically toward Signal.
Everything a program does is mediated by the Operating System Kernel to some degree. IE - cryptography sessions are handled by specific sequences of memory formating and other such things to act as a layer of security.
But … If your computer's OS is compromised out of the box, it doesn't really matter as the keys are needed to create and read the encrypted data.
Likewise, if I have a human source in the organization I need to monitor, I don't really need to have computer surveillance.
There are better ways of communicating than cryptography, however. Cryptography more or less says "I am trying to say something I don't want others to hear."