Modal dialogs are not placed on top of their respective windows

### What Happened?

Modal dialogs are not placed on top of their respective windows

### Steps to Reproduce

1. Open a folder that has some files in it with vscode
2. Try to permanently delete a file using vscode explorer, by pressing shift+delete
3. Confirmation dialog appears in top left corner, way out of where the vscode window is.

### Expected Behavior

Modal dialogs are placed on top of their respective windows.

### OS Version

8.x (Circe)

### OS Architecture

amd64 (on most hardwares)

### Session Type

Classic Session (X11)

### Software Version

Latest release (I have run all updates)

### Log Output

```shell

```

### Hardware Info

_No response_

Reproduce the problem in the VS Code Explorer by using Shift+Delete on a file, under elementary OS 8.x with an amd64 Classic X11 session. Start by tracing how Gala positions the confirmation modal relative to its parent window; done means the dialog appears on top of the respective VS Code window rather than in the top-left corner.

Written by the indexing model from the issue text.