It's true that Parck was the de facto leader of the Empire of the Hand during Thrawn's absence, however the flagship and it's commander is not necessarily the leader of the faction, just a high-up military commander; Kaine and the Reaper, for example, will likely not be the flagship for the Alignment (mostly because we don't want people to have a free Executor), and Ackbar with Home One serve as the flagship, as opposed to Mon Mothma for the New Republic. The choice for the Empire of the Hand is between Parck in the Adminitor, Stent in Thrawn's Hand, and Siath in the Battlehammer. The main reason not to do Parck is because if we did him and the Admonitor, that means three of the four factions have their flagship as an ISD, and we'd prefer some variety.