### 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)

struct {
				float points[6]; 
				float uvs[6]; 
				uint32_t colors[6]; 
			};
		};
		uint32_t flags;
		uint32_t specular_shininess;
		uint32_t lights[4];
	};
	struct Data {
		GLuint canvas_quad_vertices;
		GLuint canvas_quad_array;
		GLuint indexed_quad_buffer;
		GLuint indexed_quad_array;
		GLuint particle_quad_vertices;
		GLuint particle_quad_array;
		GLuint ninepatch_vertices;
		GLuint ninepatch_elements;
		RID canvas_shader_default_version;
		uint32_t max_lights_per_render = 256;
		uint32_t max_lights_per_item = 16;
		uint32_t max_instances_per_buffer = 16384;
		uint32_t max_instance_buffer_size = 16384 * 128;
	} data;
	struct Batch {
		
		uint32_t start = 0;
		uint32_t instance_count = 0;