Godot 4 freezing when saving files on Linux running X11 or XWayland DisplayServer with multiple windows (ProgressDialog window issue?)

### Tested versions

- Tested In Godot 4.0 stable and 4.2.1 Stable

### System information

Godot v4.2.1.stable - Ubuntu 22.04.4 LTS 22.04 - Wayland - GLES3 (Compatibility) - Mesa Intel(R) HD Graphics (BYT) () - Intel(R) Celeron(R) CPU N2806 @ 1.60GHz (2 Threads)

### Issue description

Sometimes When I Try To Save A Scene, Or Creating A Script To A Node, Godot Just Randomly Freezes And Becomes Unusable. It Usually Happens When I Try To Save A Scene, But It Also Happened When I Tried Creating A Script Or Saving A Node As A Scene. ( Godot 3.6-beta4 and below work as intended )

[Screencast from 07-04-2024 18:38:56.webm](https://github.com/godotengine/godot/assets/67060689/ebfe58cd-0e8b-4dbf-9ce8-97744aad42bc)

### Steps to reproduce

- Open Godot 4.0 stable or Above
- Load A Project
- Save A Scene/Create A Script
- Bug Happens

### Minimal reproduction project (MRP)

N/A

### --verbose Output
[Godot Log.txt](https://github.com/godotengine/godot/files/14972400/Godot.Log.txt)