### 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)

} else {
			gui.subwindow_focused = nullptr;
		}
	}
	RenderingServer::get_singleton()->viewport_set_parent_viewport(p_window->viewport, p_window->parent ? p_window->parent->viewport : RID());
}
int Viewport::_sub_window_find(Window *p_window) const {
	for (int i = 0; i < gui.sub_windows.size(); i++) {
		if (gui.sub_windows[i].window == p_window) {
			return i;
		}
	}
	return -1;
}
void Viewport::_update_viewport_path() {
	if (viewport_textures.is_empty()) {
		return;
	}
	Node *scene_root = get_scene_file_path().is_empty() ? get_owner() : this;
	if (!scene_root && is_inside_tree()) {
		scene_root = get_tree()->get_edited_scene_root();
	}
	if (scene_root && (scene_root == this || scene_root->is_ancestor_of(this))) {
		NodePath path_in_scene = scene_root->get_path_to(this);
		for (ViewportTexture *E : viewport_textures) {
			E->path = path_in_scene;
		}
	}
}
void Viewport::_notification(int p_what) {