I agree with Morpheus
...Alto could really just switched vf or put his plan to motion when Klan bought him some time.
There were no smoke trails from Alto's ship when he came back, no face shots either. Plus, when he maneuvred behind the wreckage it looks as if he stopped there, between http://i34.tinypic.com/28tuc09.jpg and http://i36.tinypic.com/314rmmq.jpg there's more than enough time to show his vf coming back, but its just not there
The only things pointing that it was Alto was the red highlights and his voice calling out to Klan before he... gets owned XD
Explains the command centre update. Just another theory