First, please pay attention to where you're posting stuff; this section is for Ascendancy, our Sins mod, not for Imperial Civil War, which is directly below it.
Obviously Corey is talking about before he moved your thread into the right section (where it is now).
Just a quick note, if you're referring to a specific video it would be helpful if you posted a link to the actual video, and not just to your friend's channel (which obviously our Youtube embedding code gets confused by). In any case I assume it's the
Empire of the Hand Episode 6 video we're talking about here?
The answer to your question is that the appearance of Thrawn in Imperial Remnant service is perfectly normal behaviour:
In our progressive Galactic Conquests (Art of War, Essence of War, Imperial Civil War) the death of the Imperial leader (killed by any faction) causes the era to advance and changes the hero and unit rosters for each faction. The Imperial faction starts with Admiral Isard, with Grand Admiral Thrawn leading the Empire of the Hand. When Isard is killed Thrawn is removed from the Empire of the Hand and is added as the new leader of the Imperial Remnant, reflecting canonical events between the Battle of Endor (Episode VI) and Timothy Zahn's Thrawn trilogy. When the Imperial Remnant's Thrawn is killed the era advances again with the Reborn Emperor appearing (followed by Admiral Daala and Grand Admiral Pellaeon to complete the era sequence).
If you want to learn more about the era mechanics please see the mod manual which gives details about the various units, heroes, GCs and eras in the mod.