After switching from gesture navigation to button navigation, booting into safe mode, toggling the toolbar, rebooting and changing the navigation back to gesture-based: the flip toolbar now appears in some 3rd party apps (signal, gcam, threema) and when the flashlight is on. Which largely solves my problem.
It doesn't appear when the default camera app is used or in apps that make OS requests to take a picture/record media (see:
https://developer.android.com/reference/android/provider/MediaStore#ACTION_IMAGE_CAPTURE for a deep dive) as opposed to apps implementing their own interface with the camera2 Api