How to reproduce:
1. Create a new Unity project
2. Create a GameObject with a child and turn it into a Prefab
3. In the Hierarchy window add a new child to the Prefab
4. Without applying the override open the Prefab in Prefab Mode
5. Add a new child to the Prefab
6. Exit Prefab Mode and see the Hierarchy window

Expected result: the unapplied child GameObject override is positioned at the bottom
Actual result: the unapplied child GameObject override is positioned in the middle

Reproducible with: 2018.3.0a6, 2018.4.7f1, 2019.2.4f1, 2019.3.0b1, 2020.1.0a2
Could not test with: 2017.4.32f1, 2018.3.0a5(Uses the old Prefab System)

Notes:
Same structural result can be achieved by applying new child GameObject overrides individually
The unapplied child GameObject can be moved down, but cannot be moved up
The Overrides menu shows not only the added child, but also indistinct changes in Transform for children, positioned lower than the unapplied child override; applying the Transform changes does nothing and retains the entry in the 'Overrides' menu