That was my first thought. This is how they kill Signal. It was how they killed Skype. Take a P2P communication system that is difficult to spy on, give Microsoft a big pile of money on the sly to buy it and re-engineer it to be a centralized system and restore spy-ability. It almost seems so laughably obvious as to be childishly unwise to attempt.
How would Signal working with Microsoft to implement the Signal protocol in Skype somehow kill Signal?
Signal (the organization) has worked with other companies, like Facebook and WhatsApp (owned by FaceBook, I know), to implement the Signal protocol on their respective messaging services. It appears that's precisely what they're doing with Skype in this case. It's not like Microsoft is buying out Signal.