Matrix also does have a pretty big problem with meta data. By default it stores a ton of meta data (at least the reference server implementation does) and I am not sure if this is even a solvable problem without redesigning the protocol. When opting for an alternative to Signal, XMPP is probably the better choice.

I’d choose LUKS over Veracrypt for simplicity. If the drive is solely for backup, depending on the backup tool you use, you might not even need encryption on the file system level. Several backup solutions support data encryption.