Maybe they have an 'understanding' about the implementation of the cryptography as they do with WhatsApp, meaning the program doesn't notify you when your opposite's keys change, leaving unscrupulous users (most) susceptible to MitM attacks, which could be used by law enforcement or three-letter-agencies.
Plus, Skype probably still makes extensive use of meta-data, Signal allege that they don't, but we can't really assess what's actually running on their servers, despite the use of the AGPL.