### 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)

state.instance_data_array[r_index].dst_rect[i] = 0.0;
			state.instance_data_array[r_index].lights[i] = uint32_t(0);
		}
		state.instance_data_array[r_index].color_texture_pixel_size[0] = 0.0;
		state.instance_data_array[r_index].color_texture_pixel_size[1] = 0.0;
		state.instance_data_array[r_index].pad[0] = 0.0;
		state.instance_data_array[r_index].pad[1] = 0.0;
		state.instance_data_array[r_index].lights[0] = lights[0];
		state.instance_data_array[r_index].lights[1] = lights[1];
		state.instance_data_array[r_index].lights[2] = lights[2];
		state.instance_data_array[r_index].lights[3] = lights[3];
		state.instance_data_array[r_index].flags = base_flags | (state.instance_data_array[r_index == 0 ? 0 : r_index - 1].flags & (FLAGS_DEFAULT_NORMAL_MAP_USED | FLAGS_DEFAULT_SPECULAR_MAP_USED)); 
		Color blend_color = base_color;
		GLES3::CanvasShaderData::BlendMode blend_mode = p_blend_mode;
		if (c->type == Item::Command::TYPE_RECT) {
			const Item::CommandRect *rect = static_cast<const Item::CommandRect *>(c);
			if (rect->flags & CANVAS_RECT_LCD) {
				blend_mode = GLES3::CanvasShaderData::BLEND_MODE_LCD;
				blend_color = rect->modulate * base_color;
			}
		}
		if (blend_mode != state.canvas_instance_batches[state.current_batch_index].blend_mode || blend_color != state.canvas_instance_batches[state.current_batch_index].blend_color) {
			_new_batch(r_batch_broken);
			state.canvas_instance_batches[state.current_batch_index].blend_mode = blend_mode;
			state.canvas_instance_batches[state.current_batch_index].blend_color = blend_color;
		}
		switch (c->type) {
			case Item::Command::TYPE_RECT: {
				const Item::CommandRect *rect = static_cast<const Item::CommandRect *>(c);
				if (rect->flags & CANVAS_RECT_TILE && state.canvas_instance_batches[state.current_batch_index].repeat != RenderingServer::CanvasItemTextureRepeat::CANVAS_ITEM_TEXTURE_REPEAT_ENABLED) {