Reproduction steps:
1. Create a new project
2. After Editor loads shut it down completely
3. Open project root and navigate to Library folder
4. Replace "CurrentLayout-default.dwlt" with the one attached in edits
5. Open the project again
6. In the scene create a new empty GameObject at (0, 0, 0)
7. Attach the "SceneGUIExample.cs" script to the object
8. Select the GameObject and inspect the Scene

Expected result: OnSceneGui is called and there is a rectangle wireframe in the scene at GameObject's position
Actual result: OnSceneGui is not called and there is no rectangle wireframe in the scene GameObject's position

Reproducible with: 2021.1.15f1
Not reproducible with: 2018.4.36f1, 2019.4.29f1, 2020.3.14f1, 2021.2.0b4, 2022.1.0a3

Note:
1. looking at a diff tool the layout file where the issue reproduces is mostly different in some of the values (not by a great margin). Some lines seem to be missing, though the file does not appear corrupted or anything of the sort.
2. I am not sure if the issue here is OnSceneGui not working with the layout, or the layout being somehow edited during the game creation process so that the issue starts reproducing.
3. An upgrade of the project might resolve the issue, but I did not find it consistent