Embedded game draws over progress dialog on platforms where a floating window is used for game embedding

### Tested versions

- Reproducible in godot v4.4rc3

### System information

Windows 11, Multi window mode

### Issue description

Embedded game draws over "loading state" and notifications:

https://github.com/user-attachments/assets/43ce9d2a-c109-4b4f-8352-b4a8cac9a36c

https://github.com/user-attachments/assets/5bf6e8a1-4b2a-4c28-96af-5436ffe00f12

### Steps to reproduce

- Run scene
- Click build project
- Or import something

### Minimal reproduction project (MRP)

N/A

Start by reproducing the issue on Windows 11 with Godot v4.4rc3 in multi-window mode, following the build-project or import steps. There is no minimal reproduction project or file, test, or entry point named in the report. Done means the embedded game no longer draws over the loading state and notifications when floating-window embedding is used.

Written by the indexing model from the issue text.