### 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)

case SUB_WINDOW_RESIZE_BOTTOM: {
						diff.y = MAX(diff.y, -limit.y);
						r.size.y += diff.y;
					} break;
					case SUB_WINDOW_RESIZE_BOTTOM_RIGHT: {
						diff.x = MAX(diff.x, -limit.x);
						diff.y = MAX(diff.y, -limit.y);
						r.size += diff;
					} break;
					default: {
					}
				}
				Size2i max_size = gui.currently_dragged_subwindow->get_max_size();
				if ((max_size.x > 0 || max_size.y > 0) && (max_size.x >= min_size.x && max_size.y >= min_size.y)) {
					max_size.x = MAX(max_size.x, 1);
					max_size.y = MAX(max_size.y, 1);
					if (r.size.x > max_size.x) {
						r.size.x = max_size.x;
					}
					if (r.size.y > max_size.y) {
						r.size.y = max_size.y;
					}
				}
				gui.currently_dragged_subwindow->_rect_changed_callback(r);
			}
			if (gui.currently_dragged_subwindow) { 
				_sub_window_update(gui.currently_dragged_subwindow);
			}
		}
		return true;