Your IP address is public so every time you consult a website, there is a number of actors (in addition to the final website) seeing your IP in their connection logs: ISP/routers/trackers/CDN and more. PeerTube is transparent about it: we warn you that if you want to keep your IP private, you must use a VPN or Tor Browser. Thinking that removing P2P from PeerTube will give you back anonymity doesn't make sense.
Two factor authentication adds an additional layer of security to your account by requiring a numeric code from another device (most commonly mobile phones) when you log in.