### 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.mouse_focus_mask.set_flag(mouse_button_to_mask(mb->get_button_index()));
				if (mb->get_button_index() == MouseButton::LEFT) {
					gui.drag_accum = Vector2();
					gui.drag_attempted = false;
				}
			}
			DEV_ASSERT(gui.mouse_focus);
			mb = mb->xformed_by(Transform2D()); 
			Point2 pos = gui.mouse_focus->get_global_transform_with_canvas().affine_inverse().xform(mpos);
			mb->set_position(pos);
#ifdef DEBUG_ENABLED
			if (EngineDebugger::get_singleton()) {
				Array arr;
				arr.push_back(gui.mouse_focus->get_path());
				arr.push_back(gui.mouse_focus->get_class());
				EngineDebugger::get_singleton()->send_message("scene:click_ctrl", arr);
			}
#endif
			if (mb->get_button_index() == MouseButton::LEFT) { 
				CanvasItem *ci = gui.mouse_focus;
				while (ci) {
					Control *control = Object::cast_to<Control>(ci);
					if (control) {
						if (control->get_focus_mode() != Control::FOCUS_NONE) {
							if (control != gui.key_focus) {
								control->grab_focus();
							}
							break;
						}
						if (control->data.mouse_filter == Control::MOUSE_FILTER_STOP) {