Project manager window dissappear when launching from Hyprland, but works fine from VSCode

[Nikitf777]

Tested versions

Reproductible in 7b1ed52 and #99119
Not reproductible in 4.3 branch

System information

Godot v4.4.beta (7b1ed52) - CachyOS Linux #1 SMP PREEMPT_DYNAMIC Thu, 09 Jan 2025 20:57:06 +0000 on Wayland - X11 display driver, Multi-window, 1 monitor - Vulkan (Forward+) - integrated AMD Radeon Graphics (RADV GFX1103_R1) (Radeon 780M) - AMD Eng Sample (16 threads) (Ryzen 7 8845HS)

Issue description

Recently I tried to compile the #99119 PR on my new mini PC with CachyOS and Hyprland. Compilation went successful, but for some reason project manager window just dissappear after the loading screen (even when launching it from the Editor by executing the binary with the --editor flag and pressing the "Quit to Project List" button). Then I tried to compile master (which is currently 7b1ed52) and the result was the same. The same issue applies to precompiled binary of the 4.4 Beta 1.
Then I tried to debug it from VSCode. I created launch.json file, launched the executable and, surprisingly, the project manager appears on my screen. Then I tried to execute it from the GNOME shell, which also was successful.
Also, I figured out that enabling "Prefer Wayland" in the Editor settings fixes the bug.

For me, it looks more like a Hyprland and/or XWayland issue, but why is it reproductible only in 4.4 then? And why can it be so easily fixed by just launching the Godot Project Manager from VSCode? Maybe it also can be fixed by Godot itself?

P.S. I recompiled again, but this time it doesn't work correctly even from VSCode.

Steps to reproduce

1. Download or compile 4.4
2. Launch it NOT from VSCode.

Minimal reproduction project (MRP)

No project needed.