### Godot version

4.1.1 stable

### System information

Windows 10

### Issue description

this is the default size loaded on startup 1024 which seems fine but it actually have loaded the default [2048] and ignored the size in project settings
![image](https://github.com/godotengine/godot/assets/53877170/c8c71de7-468a-487f-8e6c-dba1ce0f8fa5)

changing it now to any size will break it 
[2048]
![image](https://github.com/godotengine/godot/assets/53877170/3082ff09-b7d7-41f7-8fbb-813074a54135)

[512]
![image](https://github.com/godotengine/godot/assets/53877170/5ea4620f-52b5-4d0e-a5f5-747e777cd59d)


### Steps to reproduce

change 2d shadow atlas size in project settings while using compatibility renderer. 

### Minimal reproduction project

_
state.instance_data_array[r_index].color_texture_pixel_size[0] = texpixel_size.x;
				state.instance_data_array[r_index].color_texture_pixel_size[1] = texpixel_size.y;
			} break;
			case Item::Command::TYPE_POLYGON: {
				const Item::CommandPolygon *polygon = static_cast<const Item::CommandPolygon *>(c);
				
				_new_batch(r_batch_broken);
				state.canvas_instance_batches[state.current_batch_index].tex = polygon->texture;
				state.canvas_instance_batches[state.current_batch_index].command_type = Item::Command::TYPE_POLYGON;
				state.canvas_instance_batches[state.current_batch_index].command = c;
				state.canvas_instance_batches[state.current_batch_index].shader_variant = CanvasShaderGLES3::MODE_ATTRIBUTES;
				_prepare_canvas_texture(polygon->texture, state.canvas_instance_batches[state.current_batch_index].filter, state.canvas_instance_batches[state.current_batch_index].repeat, r_index, texpixel_size);
				state.instance_data_array[r_index].modulation[0] = base_color.r;
				state.instance_data_array[r_index].modulation[1] = base_color.g;
				state.instance_data_array[r_index].modulation[2] = base_color.b;
				state.instance_data_array[r_index].modulation[3] = base_color.a;
				for (int j = 0; j < 4; j++) {
					state.instance_data_array[r_index].src_rect[j] = 0;
					state.instance_data_array[r_index].dst_rect[j] = 0;
					state.instance_data_array[r_index].ninepatch_margins[j] = 0;
				}
				_add_to_batch(r_index, r_batch_broken);
			} break;
			case Item::Command::TYPE_PRIMITIVE: {
				const Item::CommandPrimitive *primitive = static_cast<const Item::CommandPrimitive *>(c);
				if (primitive->point_count != state.canvas_instance_batches[state.current_batch_index].primitive_points || state.canvas_instance_batches[state.current_batch_index].command_type != Item::Command::TYPE_PRIMITIVE) {
					_new_batch(r_batch_broken);
					state.canvas_instance_batches[state.current_batch_index].tex = primitive->texture;
					state.canvas_instance_batches[state.current_batch_index].primitive_points = primitive->point_count;
					state.canvas_instance_batches[state.current_batch_index].command_type = Item::Command::TYPE_PRIMITIVE;