They're opening up the protocol so that any website can provide the authentication, and Mastodon already implements it: if you have an account on Mastodon, you can have an additional proof on keybase.
See the blog post and the spec that details the changes to implement: https://keybase.io/blog/keybase-proofs-for-mastodon-and-ever...
I presume a pure IM system would have to implement some web gateway at the server level.