I have made more tests about this issue and it is still present. I remove all atf textures from my game and only left one theme texture atlas which is regular png.
I have recorded how my stripped version of game where only UI is shown look like:
I was recorded on iPhone X
And here is the Adobe Scout profile for that session:
You can see how performance of Context3D.clear changes. I think that any change in rendering triggers it. And it can trigger it to be slow or to be normal. It is probably a timing issue like Daniel have suggested.
Can you please create something similar and test on your iPhone 7. Basically what I have done is I just created a StackScreenNavigator. And I have 3 screens. On 2 screens I only display buttons and on the 3rd screen I display list with TiledRow layout.