Reproduction steps:
1. Open attached project "DanglingWarning.zip" and scene "SampleScene"
2. In Hierarchy window, select "Cube" Prefab
3. In Inspector window, add any new Component
4. In Inspector window's Overrides dropdown, click Apply All
5. Undo
6. Redo
7. Observe Console window

Expected result: No warning
Actual result: "Component of type <...> was added to Cube using GameObject.AddComponent() and had become dangling during an undo operation.
Use Undo.AddComponent to correctly add a component which can be handle by the undo system" warning

Reproducible with: 2021.2.0a9, 2021.2.0b16, 2022.1.0a11
Not reproducible with: 2019.4.30f1, 2020.3.19f1, 2021.1.23f1, 2021.2.0a8, 2022.1.0a12