Yes SwiftKey is compatible with external physical (Bluetooth) keyboards.
However in order to get the most out of your external keyboard, the following points should be noted:
1 - How to hide the SwiftKey Keyboard
Your virtual SwiftKey Keyboard will remain onscreen when a Bluetooth keyboard is connected.
Fortunately it's easy to hide the virtual keyboard - some apps will allow you to use a swipe gesture to close the keyboard. E.g. in the iPhone Messages app swipe down from your messages and into your keyboard area, for Gmail swipe downwards in an email and into your keyboard area.
2 - Language/Layout settings
You will find that Language/Layout settings for your external keyboard live outside of the SwiftKey app.
Instead, on your device head to Settings > General > Keyboard > Hardware Keyboard
Check that the keyboard for your region/locale is selected. In most cases it will be set to 'Automatic' by default.
Inserting apostrophes and special characters
By making sure your external keyboard is configured correctly, you shouldn't have any trouble typing special characters or punctuation.