Sorry for my ignorance but I don't understand how that's the case? As you've stated masterdon doesn't follow activitypub 100%, would would be stopping twitter from keeping their private chat between twitter users (or even adopting another open protocol such as matrix) whilst moving their public facing stuff to activitypub?
Twitter has "private accounts," which are accounts that have restricted followers, and only allow posting to followers. This is fine with Twitter's way of doing things, however breaks in a federated world.
Matrix is bad for many reasons, but it's not a direct fix over this problem more than a band-aid.
Keeping private stuff centralized would be reasonable, but they're not going to do it: expecting large entities to handle something like this with surgical precision rather than a sledgehammer is unrealistic.
