It's how it was designed from the get-go. Godot started off as an engine for a relatively narrow focus, being used internally at a company that was using it to developer their game. Initially, it was very feature-limited, having only a 2D renderer. The developers kept it very lean, and focused more on its structure and tools as opposed to trying to expand its feature set.
Since then, it's kept a lot of that lower-scale, leaner focus. Additional features have been added incrementally, with prioritization going toward flexibility and usability over flashy features. This has kept it very light-weight. I often compare Godot to Blender. Blender isn't quite as feature-rich as 3D Studio Max, Maya 3D, etc... But it is way smaller, and provides an enormous amount of potential for its minuscule footprint.
The motivation behind the project also helps. Godot isn't a commercial engine anymore. It doesn't have to attempt to sell itself, so the community and project leaders developing it don't have to cram it full of features to make it more appealing. They can maintain a different focus.
