### Godot version

4.1.1-stable

### System information

Windows 10

### Issue description

When the project loads in editor, all the settings defined in project settings will be loaded over the default values, but when running the game nearly 95% of them will be ignored resulting in just loading the default settings.

here it's just loading only 4 variables from project setting and i have added the fifth in this pull request https://github.com/godotengine/godot/pull/80151
![image](https://github.com/godotengine/godot/assets/53877170/926168a6-e6d3-4983-b59d-7fd202db681d)

_EIDX(2, 3), _EIDX(2, 2), _EIDX(1, 2),
			
			_EIDX(2, 0), _EIDX(2, 1), _EIDX(3, 1),
			_EIDX(3, 1), _EIDX(3, 0), _EIDX(2, 0),
			_EIDX(2, 1), _EIDX(2, 2), _EIDX(3, 2),
			_EIDX(3, 2), _EIDX(3, 1), _EIDX(2, 1),
			_EIDX(2, 2), _EIDX(2, 3), _EIDX(3, 3),
			_EIDX(3, 3), _EIDX(3, 2), _EIDX(2, 2),
			
			_EIDX(1, 1), _EIDX(1, 2), _EIDX(2, 2),
			_EIDX(2, 2), _EIDX(2, 1), _EIDX(1, 1)
		};
#undef _EIDX
		glBufferData(GL_ELEMENT_ARRAY_BUFFER, sizeof(elems), elems, GL_STATIC_DRAW);
		glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, 0);
	}
	int uniform_max_size = config->max_uniform_buffer_size;
	if (uniform_max_size < 65536) {
		data.max_lights_per_render = 64;
	} else {
		data.max_lights_per_render = 256;
	}
	
	data.max_instances_per_buffer = uint32_t(GLOBAL_GET("rendering/gl_compatibility/item_buffer_size"));
	data.max_instance_buffer_size = data.max_instances_per_buffer * sizeof(InstanceData); 
	state.canvas_instance_data_buffers.resize(3);
	state.canvas_instance_batches.reserve(200);
	for (int i = 0; i < 3; i++) {
		GLuint new_buffers[3];
		glGenBuffers(3, new_buffers);