I really do not believe that Morale should work anything like the way they set it up. The biggest factor that affects the unity factor -- which is how Stardock is describing Morale = "patriotism" -- is communication. Which for a high-tech civilization is at least as fast as the fastest ships in the empire's Navy. With a good possibility of eventually creating an instantaneous comm network that connects the planets farthest from each other.
Think of it this way: Take the British empire or the United States as it sprawled across North America. Despite communications that could take weeks to get a message from coast to coast, or from India to the Home Office in London. Despite that comm lag, citizens at the extreme ends nonetheless came to think of themselves as being citizens of the Empire. Proud to be British whether in London, South Africa, India, Hong Kong, et al. Or citizens in Portland, ME or Portland, OR, or Anchorage, AK or even in Puerto Rico ALL thought of themselves as "Americans" first and foremost. Where's the Morale hit in that where the individual citizens are obviously tiny little outposts of Empire, scattered across vast distances?
The real Morale adjustments generally came from 1) events that were so significant as to be of interest across the entire empire. ("Remember the Alamo!", "Remember the Maine!", "Remember the Lusitania!", "Remember Pearl Harbor!", etc.) And 2) unpopular governmental policies that affect specific citizens. ("No taxation without representation!") In the case of GC3, such events would be pursuing an unpopular war, winning or losing significant battles, bread-and-circuses, advances in propaganda/brainwashing, etc.
Given instantaneous or near-instantaneous communications, I see no reason why an honest-to-goodness star empire couldn't span 10,000 colonies. But using GC3's Morale formulas, getting past 200 would be effectively impossible without the whole system falling to pieces.