Improve PackedScene instantiate

Make `resource_local_to_scene` behave as described in the documentation. (If I understand correctly, the following **instance** refers to **the instance of the sub-scene**.)
https://github.com/godotengine/godot/blob/2e24b76535dceb9cf18ab8ece3304ed92948c1b5/doc/classes/Resource.xml#L70-L72

If the resources of the sub-scene are modified in the main scene, the modified resources will be recorded in the `tscn` file of the main scene. And the root node of the sub-scene will be set twice.
1. In the main scene, when encountering a sub-scene, the sub-scene will be initialized first;
2. Then use the resources in the main scene to reset the root node of the sub-scene.

This may make `resource_local_to_scene` not work as expected. The resources cannot be shared between the sub-scene root node and other ordinary nodes in the sub-scene.

Yes, if the resources have `resource_local_to_scene` enabled, this patch treats the modified resources of the sub-scene root node as resources in the sub-scene, not in the main scene. Although the modifications are recorded in the `tscn` file of the main scene.

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