I'm not sure if I understand what your actual question or problem is?
Is it that apt-get says the latest version is v2.9 vs. the current
v4.2? Or something else? Once Tenable moved from v3 to v4,
everything changed with their requirements for subscriptions, etc.
And to be honest, I've not installed v4.x so I don't know if they even
source it out anymore or if you need to grab the install from them
directly. The plugins can be added after the install, I believe there
is a nessus cmd to fetch the plugins.
sawall