The source code licence has nothing to do with the right to access a particular service. Additionally, the organization behind signal is not bound to the licence, they can do whatever they want with their own code, it's their code after all.
If the server code is licenced as AGPL3 that grants others particular rights in addition to those granted by regular law, under particular constraints, to use and modify said source code, and thus enables e.g. Molly to provide their own servers.
The Signal source is GPL 3.0, so definitely libre.