It's probably like that on purpose to avoid hacker trying to use a 3rd party keyboard to get into your phone. Also when you are in an app and you have to log into an account the Password Field upon pressing results in the default keyboard popping up. It all makes sense to me.
Using Swype and it doesn't work from the lock screen or in quick reply. It will also change baco to the default Apple keyboard for all apps after using quick reply.