There's a reason that they say performance is the most leaky abstraction.
I get what you are saying and it definitely applies to the core architecture of the product, but if you have a large number of customers each with their own needs then I would be surprised if there were zero parts of the product that were modular or interchangeable.
You'd be surprised. Game engines are extremely monolithic.
There are some modular components and techniques (eg pathfinding, rendering, physics engine), but most of the effort that goes into an engine like Godot is integrating these components to their specific architecture. While the component is transferable (eg you can always use the Bullet engine in your own project), the integration work isn't.