### 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)

contact_3d_debug_multimesh = RenderingServer::get_singleton()->multimesh_create();
				RenderingServer::get_singleton()->multimesh_allocate_data(contact_3d_debug_multimesh, get_tree()->get_collision_debug_contact_count(), RS::MULTIMESH_TRANSFORM_3D, false);
				RenderingServer::get_singleton()->multimesh_set_visible_instances(contact_3d_debug_multimesh, 0);
				RenderingServer::get_singleton()->multimesh_set_mesh(contact_3d_debug_multimesh, get_tree()->get_debug_contact_mesh()->get_rid());
				contact_3d_debug_instance = RenderingServer::get_singleton()->instance_create();
				RenderingServer::get_singleton()->instance_set_base(contact_3d_debug_instance, contact_3d_debug_multimesh);
				RenderingServer::get_singleton()->instance_set_scenario(contact_3d_debug_instance, find_world_3d()->get_scenario());
				RenderingServer::get_singleton()->instance_geometry_set_flag(contact_3d_debug_instance, RS::INSTANCE_FLAG_DRAW_NEXT_FRAME_IF_VISIBLE, true);
#endif 
				set_physics_process_internal(true);
			}
		} break;
		case NOTIFICATION_READY: {
#ifndef _3D_DISABLED
			if (audio_listener_3d_set.size() && !audio_listener_3d) {
				AudioListener3D *first = nullptr;
				for (AudioListener3D *E : audio_listener_3d_set) {
					if (first == nullptr || first->is_greater_than(E)) {
						first = E;
					}
				}
				if (first) {
					first->make_current();
				}
			}
			if (camera_3d_set.size() && !camera_3d) {
				
				Camera3D *first = nullptr;
				for (Camera3D *E : camera_3d_set) {
					if (first == nullptr || first->is_greater_than(E)) {