In MetaTune, the Key/Scale changes are recorded on the notes automation lanes. This allows for custom scale automations.
To change the Key/Scale using automation in MetaTune, you'll need to change the Automation mode of the track to "Write" and select the Key/Scale during playback (like you would do for any other parameter). When this happens, you'll notice the automation lanes of each individual note change to On and Off respectively.
Changing the track automation mode is a little different in each DAW, but as an example, you can see how to automate the Key/Scale in Logic Pro: