### 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)

Rect2 swrect = Rect2i(sw->get_position(), sw->get_size());
					if (!sw->get_flag(Window::FLAG_BORDERLESS)) {
						int title_height = sw->get_theme_constant(SNAME("title_height"));
						swrect.position.y -= title_height;
						swrect.size.y += title_height;
					}
					if (swrect.has_point(viewport_pos)) {
						viewport_under = sw;
						viewport_pos -= sw->get_position();
					}
				}
				if (!viewport_under) {
					
					viewport_under = embedder;
				}
			} else {
				
				Vector2i screen_mouse_pos = DisplayServer::get_singleton()->mouse_get_position();
				DisplayServer::WindowID window_id = DisplayServer::get_singleton()->get_window_at_screen_position(screen_mouse_pos);
				if (window_id != DisplayServer::INVALID_WINDOW_ID) {
					ObjectID object_under = DisplayServer::get_singleton()->window_get_attached_instance_id(window_id);
					if (object_under != ObjectID()) { 
						Window *w = Object::cast_to<Window>(ObjectDB::get_instance(object_under));
						if (w) {
							viewport_under = w;
							viewport_pos = screen_mouse_pos - w->get_position();
						}
					}
				}
			}