Extension EditorPlugins added during Hot Reload on Initialization level Editor were being attached to the scene tree before all the GDExtension Classes (such as already loaded resources) are re-initialized.

In general, the order of the operations looked like so:

0. Hot reload starts
1. Godot starts unloading extension. (we unregister existing EditorPlugin at this point)
2. Godot caches all the properties on present instances & turns all the gdextension classes into native classes (GDExtension Class inheriting Resource -> Resource and so on)
3. Godot starts (re)initalizing the library – Extension registers all the classes etc
4. on the end of the initialization we run editor_add_plugin - which was instantly adding EditorPlugin to the tree, launching its lifecycle methods.
5. enter_tree() – we were still in hot reload and any GDExtension class instance at this point is represented by its base class – i.e. loading any previously initialized GDExtension Resource will return "bare" resource.
6. After initialization – and launching startup callbacks – Godot finishes hot reload, changes all the aforementioned instances back to the Extension Classes and puts back all the cached properties.

Related godot-rust issue: godot-rust/gdext#1132
Thread on Godot contributors chat: https://chat.godotengine.org/channel/gdextension?msg=N2sbbbuw4Z33pacWF