Can't find a number of methods for PhysicsServer3D, MessageQueue and SceneTree

I've been trying to replicate something like [this proof of concept](https://github.com/godotengine/godot/pull/49976) to add a `Physics.simulate()` for myself as an extension to use in a project and I am having issues finding the corresponding methods/classes used:
- `PhysicsServer3D::step()` and `PhysicsServer3D::flush_queries()`
- `MessageQueue` and `MessageQueue::get_singleton()` and `MessageQueue::flush()`
- `SceneTree::get_singleton()` and `SceneTree::flush_transform_notifications()`

Do these exist? Should they exist? Is there any way I can help add them? Maybe I am missing something very simple, or they are not intended to be implemented, but I cannot currently find any documentation or clear steps on how to add new methods to the API, nor a clear description of what kinds of methods should be supported.

Please let me know if I am out of bounds in my line of questioning, but the ability to do something along the lines of a `Physics.simulate()` is fairly core to some of the features our team will be working on in the near future, so I will be continuing to look into alternatives either way.

Commencez par lire la pull request de preuve de concept liée et recherchez PhysicsServer3D, MessageQueue et SceneTree dans les bindings de godot-cpp. Déterminez si les méthodes listées existent dans l’API prise en charge et ce que les recommandations du projet indiquent au sujet de leur exposition ; le travail est terminé lorsqu’une décision documentée et exploitable a été prise quant à l’ajout de ces méthodes et à la manière de procéder.

Rédigé par le modèle d'indexation à partir du texte de l'issue.