### 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)

mm->set_position(pos);
			Control::CursorShape cursor_shape = Control::CURSOR_ARROW;
			{
				Control *c = over;
				Vector2 cpos = pos;
				while (c) {
					if (!gui.mouse_focus_mask.is_empty() || c->has_point(cpos)) {
						cursor_shape = c->get_cursor_shape(cpos);
					} else {
						cursor_shape = Control::CURSOR_ARROW;
					}
					cpos = c->get_transform().xform(cpos);
					if (cursor_shape != Control::CURSOR_ARROW) {
						break;
					}
					if (c->data.mouse_filter == Control::MOUSE_FILTER_STOP) {
						break;
					}
					if (c->is_set_as_top_level()) {
						break;
					}
					c = c->get_parent_control();
				}
			}
			ds_cursor_shape = (DisplayServer::CursorShape)cursor_shape;
			bool stopped = over->can_process() && _gui_call_input(over, mm);
			if (stopped) {
				set_input_as_handled();
			}
		}