Second "Files have been modified on disk" dialog not focused

### Tested versions

4.x

### System information

Godot v4.3.stable - macOS 13.0.1 - Vulkan (Mobile) - integrated Apple M1 - Apple M1 (8 Threads)

### Issue description

When reloading a project that has changed on disk, two "Files have been modified on disk" dialogs are generated rather than one; and the second is not focused, requiring an extra click to clear it.

You can repro this just by `touch`ing files in a terminal, but in practice I run into this every time I change git branches via the terminal.

### Steps to reproduce

1. Open a project in Godot.
2. Open 2 scenes and 2 scripts in the editor.
3. In a terminal, `touch` those .tscn and .gd files.
4. Switch back to Godot.
5. Two "Files have been modified on disk" popups appear on top of each other - one for scripts, and one for scenes and settings files.
6. Mouse-click "Discard" in the topmost popup.

**Expected behavior:**
The second popup is focused, so you can click "Discard" in that as well to get back to work.

**Actual behavior:**
The Godot window is focused, and the second popup (blocking the godot window) is blurred. You must click once to focus it, and then you can click "Discard".

**An even better expected behavior:**
The two dialogs are merged into one containing all changed files, so a single "Discard" click dismisses them all.

### Minimal reproduction project (MRP)

Anything with at least two scenes and two scripts.