For instance, renderers (esp. back-ends) and physics engines are already largely subsystems which are fairly separate from the rest of the game logic.
I can imagine a world where you start with a package manager, and maybe you choose one overarching framework/ecosystem which will serve as a middleware for combining nav meshes and animations etc. in the same world space, handling events etc. the same way you might choose a framework for building a web-server from several popular options.
There's no reason you need an extremely heavy-weight closed-source black-box system to serve as the foundational layer.