popup dialog boxes become unresponsive on Debian 12.9 if only gnome-core installed

### Tested versions

- Reproducible with Godot 4.4-dev7,and 4.3-stable

### System information

Debian 12.9 minimal install with gnome-core installed. Godot Engine v4.4.dev7.official.46c8f8c5c - OpenGL API 4.1 (Core Profile) Mesa 22.3.6 - Compatibility - Using Device: VMware, Inc. - SVGA3D; build: RELEASE; LLVM

### Issue description

Godot starts without error. Version Control Metadata (and other selections within a project, and sometimes time passing) cause dialog boxes to become unresponsive. In this state the main application must often be killed (SIGTERM) to exit. No error is displayed.

### Steps to reproduce

The following actions always cause the behavior:

Install fresh minimal Debian 12.9 without desktop manager or Gnome:

```
[ ] Debian desktop environment
[ ] GNOME
...
[*] Standard system utilities
```
... then `sudo apt install gnome-core`

Reboot to enable GUI, Login, Install Godot, Start Godot.

Within the **Create new project**, select **Version Control Metadata**, select radio box **None**, experience popup dialog unresponsive.

- Not reproducible on full desktop install.
- Not reproducible with LXDE windows manager.
- Not reproducible with Plasma windows manager.
- Reproducible on Debian 11.11 with minimal install and gnome-core installed, different actions required to reproduce: Within the **Create new project**, select **Version Control Metadata**, select radio box **None**, select **Create and Edit**, experience popup dialog unresponsive.

This may be a Debian specific problem with gnome-core, a reliance on something becoming deprecated in gnome-core, or other.

All tests under VirtualBox 7.0.

### Minimal reproduction project (MRP)

N/A

Start by reproducing the unresponsive popup from Create new project after selecting Version Control Metadata and the None radio box on Debian 12.9 with only gnome-core installed. Compare the behavior with a full desktop install and other window managers, then identify the environmental difference; done means these dialogs remain responsive in the reported setup without regressing the other tested environments.

Written by the indexing model from the issue text.