@faoluin @IceWolf ActivityPub was built (originally as the Pump API) to address things OStatus lacked, like private messaging. The protocol is very similar to email. Nonetheless, people assume a protocol's design is reflective of the applications they have seen, and Mastodon being the major first popular AP system definitely colored peoples' views.
And yes, there are multiple paths to what we might call "E2E" messaging in AP, though those haven't happened yet.