### 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].modulation[1] = rect->modulate.g * base_color.g;
				state.instance_data_array[r_index].modulation[2] = rect->modulate.b * base_color.b;
				state.instance_data_array[r_index].modulation[3] = rect->modulate.a * base_color.a;
				state.instance_data_array[r_index].src_rect[0] = src_rect.position.x;
				state.instance_data_array[r_index].src_rect[1] = src_rect.position.y;
				state.instance_data_array[r_index].src_rect[2] = src_rect.size.width;
				state.instance_data_array[r_index].src_rect[3] = src_rect.size.height;
				state.instance_data_array[r_index].dst_rect[0] = dst_rect.position.x;
				state.instance_data_array[r_index].dst_rect[1] = dst_rect.position.y;
				state.instance_data_array[r_index].dst_rect[2] = dst_rect.size.width;
				state.instance_data_array[r_index].dst_rect[3] = dst_rect.size.height;
				_add_to_batch(r_index, r_batch_broken);
			} break;
			case Item::Command::TYPE_NINEPATCH: {
				const Item::CommandNinePatch *np = static_cast<const Item::CommandNinePatch *>(c);
				if (np->texture != state.canvas_instance_batches[state.current_batch_index].tex || state.canvas_instance_batches[state.current_batch_index].command_type != Item::Command::TYPE_NINEPATCH) {
					_new_batch(r_batch_broken);
					state.canvas_instance_batches[state.current_batch_index].tex = np->texture;
					state.canvas_instance_batches[state.current_batch_index].command_type = Item::Command::TYPE_NINEPATCH;
					state.canvas_instance_batches[state.current_batch_index].command = c;
					state.canvas_instance_batches[state.current_batch_index].shader_variant = CanvasShaderGLES3::MODE_NINEPATCH;
				}
				_prepare_canvas_texture(np->texture, state.canvas_instance_batches[state.current_batch_index].filter, state.canvas_instance_batches[state.current_batch_index].repeat, r_index, texpixel_size);
				Rect2 src_rect;
				Rect2 dst_rect(np->rect.position.x, np->rect.position.y, np->rect.size.x, np->rect.size.y);
				if (np->texture == RID()) {
					texpixel_size = Size2(1, 1);
					src_rect = Rect2(0, 0, 1, 1);
				} else {
					if (np->source != Rect2()) {