Yes, Messenger is one of the apps Spanbox supports. Add it from the app list, sign in on Messenger's own page (WhatsApp is a QR scan), and it lands in your unified inbox next to everything else, DMs and group chats. On the free plan it just uses one of your 3 app slots.
You can even run more than one Messenger account at once, each in its own isolated session, so a work and a personal Messenger sit side by side without logging in and out.