The Empire of the Hand's soldiers in the mod are Phalanx troops, not the EotH's Stormtroopers. They had both. The personnel funneled from the Empire to the Empire of the Hand would have worn stormtrooper armour, as would several of the species native to planets thta joined the Empire of the Hand in the unknown regions, however the personnel sent to the Empire of the Hand by the Chiss would have been fthrough Thrawn's Household Phalanx, hence why the EotH infantry in the mod are "Phalanx" Troopers. The "Correct" way to do it would be to have both if we were trying to represent everything, however we only gave them the Phalanx Troopers because there's really no need for any faction to have two of what would essentially end up being the exact same types of infantry, and of the two it's better to have the unique one.
If you want to see examples of non-Stormtrooper armoured Chiss soldiers in the Empire of the Hand, read the Hand of Thrawn Duology. Really the only other book with EotH soldiers in it is Survivor's Quest, and the unit in that book (Aurek Seven) is part of the reformed version of the 501st that Thrawn made in the EotH, and that specific squad is already a hero unit.
Basically it's like saying not every New Republic soldier would be human. Obviously not, but there are things that have to be done to take into account the fact that this is a game.