Docker is not really a security boundary (unless you use something like gVisor), so it's a bit of a red herring here.

The idea is to make your app immutable and store all state in the DB. Then, with every deployment, you throw away the VM running the old version of your app and replace it with a new VM running the new version. If the VM running the old app somehow got compromised, the new VM will (hopefully) not be compromised anymore. In this regard, this approach is less vulnerable than just reusing the old VM.