One is for messaging and another one is for actual calls (video or audio). Seems like they are somewhat different things, even though they are both for communication. Otherwise we are saying we might as well have the phone app and mail app all be part of it too.
That said, you can easily initiate a FaceTime call from a conversation in the Messages app.
You can make FaceTime audio or video calls within messages. Just tap on the top of the contact and gives you the option. Or you could 3D Touch the initials or contact pic if you have one for set person on the messages main screen and it will give you the option as well.