> Why does it matter if the messages are e2e encrypted if the messages are managed on the two ends of the channel by a closed source binary that does who-knows-what.

Would you prefer your dissident messages be read by Meta Corporation or the Islamic Republic of Iran? That's the difference.

No, there's no technical difference in the sense that neither solution can be verified to be probably secure vs. third party inspection. But in the real world the specifics of who the actors are are and the tactics they are known to employ are absolutely part of the threat model.