Perhaps because FB leadership had nothing to do with the decision in the first place? When WA was acquired they maintained fierce independence and would not interact with FB unless absolutely necessary. No code was shared, WA kept its old offices away from the FB campus, they were for all intents and purposes operating as individual companies.

After WA added e2e it became politically possible within FB to add the same to Messenger (as long as it behind a few conversation gateways that made it hidden for most users) but FB leadership did _not_ support adding e2e to WA and certain groups continued to fight against adding it to Messenger because it was going to close off a channel for the ads team to pick up signal by spying on user conversations.