I agree. It seems to me that Facebook's Messenger and WhatsApp are fundamentally incompatible. With Messenger, you can open Facebook/messenger.com/your phone and see all your messages. With WhatsApp, you have no such option, as messages are not stored remotely.
For the end-user, the most "seamless" way to integrate is to adopt Messenger's approach, which will be a security loss for WhatsApp unfortunately. As other users mentioned, there is also the possibility that the end-to-end encryption will lose its default status.
I feel a lot of the comments decrying "clickbait" actually disagree with the opinion or the underlying assumptions the title conveys.
(Such as in this case the question whether or not this is a simple decision over technical details or a broader shift in strategy with consequences for the users)
I fear this feature could be easily abused by people removing the connotation of the title in the name of making it more "objective" - but by doing this, actually throwing out the reason why the article was posted.
I'm not convinced. I can't imagine the founders of both companies abruptly leaving and "contentious staff meetings" occurring about a simple decision to remove redundancies in infrastructure.
Edit:
Also note that the article describes a lot of changes that go far beyond infrastructure - notably, that users can communicate across services and that user profiles from different services might be matched. If done, they would have a lot more far-reaching relevance than technical details.
The headline is missing a key word: infrastructure