Always on top doesn't work when set in the Project Settings menu

[TandersT]

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Bugsquad note: This issue has been confirmed several times already. No need to confirm it further.

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Godot version:
Godot Engine v3.2.3.stable.mono.official

Issue description:
The project setting Always on top doesn't work proper when set in _Ready or in the Project Settings menu.
You also cant set in in an override.cfg.
It does work as intended when setting it in _EnterTree.
Note that this is in the Mono build, I'm unsure if the same issue exists in the standard version

Steps to reproduce:
Create new project,
Go to Project-settings, Display-Window, and turn on Always on Top

Minimal reproduction project:
overlay-test.zip

[Calinou]

@TandersT Which operating system(s) did you test this on? The implementation of the "always on top" functionality is OS-specific.

[TandersT]

Windows 10

[vijuarez]

Just recreated this on Linux 5.12.5-arch1-1 running Godot v3.3.1.stable.arch_linux. Project settings didn't work, but worked immediately inside _enter_tree

[nice-shot]

I also have this issue on Godot v3.3.4 stable (not mono) on windows 10.

[dilettante54]

Same issue with v3.4.stable.official [206ba70] on Win 10. Setting OS.set_window_always_on_top(true) in _enter_tree() doesn't help.

[reptofrog]

This is fixed for me with v4.0.rc3.official 7e79aead9

Fedora Linux 37 (GNOME on Wayland)