That may be the case for Instagram, which was developed separately and then acquired, and which still uses separate accounts that AFAIK can be created without a Facebook account, although they can be connected to one.

Messenger though has always just been the chat function on Facebook, which can nowadays also be used via a dedicated website/app if you like. It doesn't even have separate account infrastructure on the backend, unlike Instagram. Looks like they're getting around that by essentially creating a second Facebook account, with social media features disabled.