Both tailscale (partially open source) and nebula (entirely open source, you have to host the "lighthouses" which assist in NAT punching yourself) do this. (Also tinc.)

Yggdrasil is basically researching a replacement for BGP, so hole punching isn't a priority. (There is a 3rd party project that does something like this for Yggdrasil, but nebula is probably the better fully open source option.)