### 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)

uint32_t instance_buffer_index = 0;
		RID tex;
		RS::CanvasItemTextureFilter filter = RS::CANVAS_ITEM_TEXTURE_FILTER_MAX;
		RS::CanvasItemTextureRepeat repeat = RS::CANVAS_ITEM_TEXTURE_REPEAT_MAX;
		GLES3::CanvasShaderData::BlendMode blend_mode = GLES3::CanvasShaderData::BLEND_MODE_MIX;
		Color blend_color = Color(1.0, 1.0, 1.0, 1.0);
		Item *clip = nullptr;
		RID material;
		GLES3::CanvasMaterialData *material_data = nullptr;
		CanvasShaderGLES3::ShaderVariant shader_variant = CanvasShaderGLES3::MODE_QUAD;
		const Item::Command *command = nullptr;
		Item::Command::Type command_type = Item::Command::TYPE_ANIMATION_SLICE; 
		uint32_t primitive_points = 0;
		bool lights_disabled = false;
	};
	
	
	
	struct DataBuffer {
		Vector<GLuint> instance_buffers;
		GLuint light_ubo = 0;
		GLuint state_ubo = 0;
		uint64_t last_frame_used = -3;
		GLsync fence = GLsync();
	};
	struct State {
		LocalVector<DataBuffer> canvas_instance_data_buffers;
		LocalVector<Batch> canvas_instance_batches;
		uint32_t current_data_buffer_index = 0;
		uint32_t current_instance_buffer_index = 0;