### Godot version

v4.2.dev.custom_build [c3b0a92c3]

### System information

Debian Linux X11 Xfce

### Issue description

In the following scene tree it is not possible to write anything in `LineEditB`.
![image](https://github.com/godotengine/godot/assets/6299227/ce5f696a-d86a-402f-98f7-6a762f15543e)

I would expect, that it is possible to focus `LineEditB` with a mouse click and write into it.

Regression from #58334

### Steps to reproduce

1. Load and run MRP
2. Mouse Click into the left LineEditB
3. Type Keyboard => No letters appear in the LineEditB

Variant:

1. Load and run MRP
2. Mouse Click into the right LineEditA
3. Mouse Click into the left LineEditB
4. Type Keyboard => Letters appear in LineEditA instead of LineEditB


### Minimal reproduction project

[BugKeyInputRouting.zip](https://github.com/godotengine/godot/files/11994804/BugKeyInputRouting.zip)

if (gui.sub_windows.size() < 2) {
		return;
	}
	if (!gui.sub_windows[gui.sub_windows.size() - 1].window->get_flag(Window::FLAG_ALWAYS_ON_TOP)) {
		int index = gui.sub_windows.size() - 1;
		while (index > 0 && gui.sub_windows[index - 1].window->get_flag(Window::FLAG_ALWAYS_ON_TOP)) {
			--index;
		}
		if (index != (gui.sub_windows.size() - 1)) {
			SubWindow sw = gui.sub_windows[gui.sub_windows.size() - 1];
			gui.sub_windows.remove_at(gui.sub_windows.size() - 1);
			gui.sub_windows.insert(index, sw);
		}
	}
	for (int i = 0; i < gui.sub_windows.size(); i++) {
		RS::get_singleton()->canvas_item_set_draw_index(gui.sub_windows[i].canvas_item, i);
	}
}
void Viewport::_sub_window_register(Window *p_window) {