I'll most likely continue to use SwiftKey, as I love using the swiping feature when my phone is on my desk. I'm really happy Apple has finally allowed this.
However... I'm not really sure I'm on board with this implementation. It seems really sloppy.
I'm seeing the same behavior as the OP in regards to messages, and other things like the lack of native dictation and a simple way to switch to the emoji keyboard (I figured out that you simply have to disable the native English keyboard to have it switch back and forth between SwiftKey and emojis, but most users probably won't), are also frustrating.