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.