Menu shortcuts do not work in EditorPlugin generated windows.

### Tested versions

- Reproducible in 4.4.1 official, 4.5 beta7 official

### System information

MacOS 15.6.1 (24G90)

### Issue description

Godot menus do not work when a window created by a plugin has focus. On Mac, you can see the menu item flash, as if the shortcut was doing something, but the associated menu item is not triggered. I thought this only applied to `add_tool_submenu_item` menu item shortcuts, but it appears to be almost all shortcuts.

I found this when implementing a pop-out feature for a bottom panel control. I am essentially doing the same thing as the code below. Once the control was popped out into the window, I noticed shortcuts were not working when the window had focus.

Is there a more formal way to create an "editor window", or to make a panel that pops out?

### Steps to reproduce

* Run the MRP.
* Put the focus on the editor.
* Press `ctrl+0` (zero) and it will print a message.
* Focus on the window the plugin opened.
* Press `ctrl+0` and nothing happens. On mac you can see the "Project" menu item flash.

You can also try other menu items, most don't work while the window has focus.

### Minimal reproduction project (MRP)

Here's the only code in the project.
* It makes menu item in Project->Tools-Demo Menu->Test Menu.
* The menu item has `ctrl + 0` shortcut.
* A message is printed when the menu is clicked or the shortcut triggers the menu.
* It creates a window and adds it to itself.

```gdscript
@tool
extends EditorPlugin

var sub_menu : PopupMenu = null
var window : Window = null

func _enter_tree() -> void:
sub_menu = PopupMenu.new()
add_tool_submenu_item("Demo Menu", sub_menu)
sub_menu.index_pressed.connect(_on_sub_menu_index_pressed)

sub_menu.add_item("Test Menu", 0)
sub_menu.set_item_accelerator(0, KEY_MASK_CTRL | KEY_0)

window = Window.new()
window.size = Vector2(500, 500)
window.title = "Shortcuts Don't Work Here"
add_child(window)

func _exit_tree() -> void:
sub_menu.free()
window.free()

func _on_sub_menu_index_pressed(index):
print("menu index ", index, " triggged")
```

[EditorShortcutDemo.zip](https://github.com/user-attachments/files/22177626/EditorShortcutDemo.zip)

Start by running the attached EditorShortcutDemo.zip and reproduce ctrl+0 with focus on the editor, then on the plugin-created window. Trace how editor menu shortcuts are dispatched in each focus state; done means the shortcut triggers the menu action while the plugin window is focused, including on the reported macOS setup.

Written by the indexing model from the issue text.