I am playing with Krennic, Deathtoopers and Boba.

Boba plays whipcord to issue himself an order. Does Krennic still issue an order to the Deathtroopers via entourage even though he is not a nominated commander?

Yes. You nominate a commander to issue the orders from the command card, but Entourage is something apart from that, so in that case Krennic may still give the order to the Deathtroopers as long as the conditions are fulfilled.

Thanks!