Godot is more or less built that way. The entire node system is an abstraction over the various “servers” and you can even completely forgo it if you want, providing your own MainLoop implementation (instead of the included SceneTree implementation of MainLoop) and then just use the servers directly.
A lot of the editor features are also implemented as plugins. It’s been very easy turning the Godot editor into a custom editor for my game by writing some simple plugins