Reproduction steps:
1. Open the “QuitStripped” project
2. Open the “SampleScene” scene
3. Build And Run
4. Press “Make Application.wantsToQuit return false”
5. Press “Call Application.Quit()”
6. Observe the top left or Player.log

Expected result: “MonoBehaviour.OnApplicationQuit invoked” is not logged
Actual result: “MonoBehaviour.OnApplicationQuit invoked” is logged

Reproduced in: 2020.3.0f1, 2020.3.47f1, 2021.3.22f1, 2022.2.13f1, 2023.1.0b10, 2023.2.0a9

Reproduced using: Windows 11, macOS 13.2.1 (Intel), Ubuntu 20.04 (by the reporter), ArchLinux (by the reporter)

Workarounds: 
1. “Application.quitting” can be used instead of “MonoBehaviour.OnApplicationQuit“
2. "Application.CancelQuit" can be used inside "MonoBehaviour.OnApplicationQuit"

Notes:
1. Related old fixed bug: [https://issuetracker.unity3d.com/product/unity/issues/guid/1261125/]
2. The said bug fix only made “Application.wantsToQuit“ be invoked before “MonoBehaviour.OnApplicationQuit” but “MonoBehaviour.OnApplicationQuit” remained always being called
3. Cannot test in Play Mode because most of quitting API does not work in Editor
4. If this is by design, it should be specified in the "MonoBehaviour.OnApplicationQuit" documentation