### Godot version

v4.2.dev.custom_build [60f3b7967]

### System information

Debian Linux X11 Xfce

### Issue description

Physics Picking within a `SubViewport` happens with `InputEventMouse` even when mouse events are disabled via `SubViewportContainer.mouse_filter = Control.MOUSE_FILTER_IGNORE`

The problem is that passive hovering still happens in the `SubViewport` with `SubViewportContainer.mouse_filter = Control.MOUSE_FILTER_IGNORE`.

I assume that it is a regression from #78017.

This was initially reported as a side-effect in #79271, which got closed, because the main issue was resolved.



### Steps to reproduce

1. Load and run MRP
2. move mouse over Icon

I would expect, that the `Area2D` receives no `InputEventMouse`, however it gets `_input_event` and also mouse-entered and mouse-exited signals.

### Minimal reproduction project

[IgnorePassiveHover.zip](https://github.com/godotengine/godot/files/12044510/IgnorePassiveHover.zip)

gui.subwindow_drag_close_rect = close_rect;
					} else {
						gui.subwindow_drag = SUB_WINDOW_DRAG_MOVE;
					}
					gui.subwindow_drag_from = mb->get_position();
					gui.subwindow_drag_pos = sw.window->get_position();
					_sub_window_update(sw.window);
				} else {
					gui.subwindow_resize_mode = _sub_window_get_resize_margin(sw.window, mb->get_position());
					if (gui.subwindow_resize_mode != SUB_WINDOW_RESIZE_DISABLED) {
						if (gui.subwindow_focused != sw.window) {
							
							_sub_window_grab_focus(sw.window);
						}
						gui.subwindow_resize_from_rect = r;
						gui.subwindow_drag_from = mb->get_position();
						gui.subwindow_drag = SUB_WINDOW_DRAG_RESIZE;
						click_on_window = sw.window;
					}
				}
			}
			if (!click_on_window && r.has_point(mb->get_position())) {
				
				if (gui.subwindow_focused != sw.window) {
					
					_sub_window_grab_focus(sw.window);
				}
				click_on_window = sw.window;
			}
			if (click_on_window) {