This is what I would do. Since its an unusual case, I would get the offer from the current advisor in some sort of a writing and apply to universities with that affidavit that he has been offered a position in the same lab. I would definitely put the current advisor as a reference, but also would consider the fact that he might not write one or even write a negative recommendation. If he writes a negative recommendations, the affidavit of the offer should recify the foul playing. In order to cover the base of him not writing one, I would have one more reference in the list. But, I would definitely play innocent as long as theres a definite red flag. I think getting the offer from the present advisor in writing, email or letter, should help to explain the new universities about his situation. Good luck