Minimized window instantly re-minimizes itself when project is configured to use the Minimized window mode on startup

[Calinou]

• Related to The window minimizes itself after switching to other desktops/workspaces #82295
  and Starting game in a minimized window causes Vulkan errors #84905.

Tested versions

• Reproducible in: 4.0.3.stable, 4.1.2.stable, 4.2.1.stable, 4.3.dev b9e0223

System information

Godot v4.3.dev (d282e4f) - Fedora Linux 39 (KDE Plasma) - X11 - GLES3 (Compatibility) - NVIDIA GeForce RTX 4090 (nvidia; 550.76) - 13th Gen Intel(R) Core(TM) i9-13900K (32 Threads)

Issue description

When you configure a project to use the Minimized window mode, it starts minimized correctly. However, when you alt-tab to it or click it in the taskbar, it will show up for a split second and minimize itself again. You need to click it one more time (sometimes more) for it to show up again permanently.

This occurs with all rendering methods, both when the project is run from the editor and run from the command line. I've only tested this on Linux/X11 so far, but it's likely this issue is OS-specific.

Steps to reproduce

• Set Display > Window > Size > Mode to Minimized in the Project Settings.
• Run the project. You may need to do this several times to reproduce the issue for sure, but here it occurs 100% of the time.

Minimal reproduction project (MRP)

test_minimized.zip