Holy Roman Emperor was a title, Holy Roman Empire was a political entity, which usually is called "civ" in this game. It is also specifically a civ from the last expansion. At a time it was the main power in Europe.
Holy Roman Empire was the name used to refer to whatever the holdings of the Holy Roman Emperor were. Similarly, the King of England at one point also held lordship over Normandy and Aquitaine. While one set of holdings had a name and the other didn't, the existence of a name for the one only occurs because the papacy created the title of Holy Roman Emperor, and awarded it to whomever it thought might do the best job protecting it from being taken over by another power (such as the Lombards, the Eastern Roman Empire, or a variety of others.) Eventually the papacy lost control of the title and it became hereditary. However, the holder of this title (and the lands associated thereof) bounced around europe quite a bit. In particular, after Charlemagne it eventually ended up with the Kings of Germany (as elected by the Electors), later in Spain (Charles V and Alfonso of Castile), and eventually held by the Duke of Austria. The King of England was at one point considered as a candidate for the title/position. This is not a civilization.
The term Holy Roman Empire applies only by transitivity to any particular body of land. We must track the Emperor to know where the empire was. In particular, here's a list of emperors with the territory they ruled:
Charlemagne (France + Germany + Northern Italy)
Louis the Pious (as above)
Lothair I (N. Italy)
Louis II (Italy)
Charles II the Bald (West Francia = France)
Charles III the Fat (as Charlemagne)
Guy III of Spoleto (Duke of Spoleto and Camerino, King of Italy)
Lambert II of Spoleto (King of Italy, Duke of Spoleto and Camerino)
Arnulf of Carinthia (East Francia = Germany)
Louis III the Blind (King of Provence and Italy)
Berengar of Friuli (Margrave of Friuli, King of Italy)
---~40 year break---
Otto I (Germany) (start Ottonian)
Otto II
Otto III
Henry II
Conrad II (Start Salian)
Henry III
Henry IV
Henry V
Lothair III (only Supplinburger)
Frederick I Barbarossa (start Hohenstaufens)
Henry VI
Otto IV of Brunswick (House of Welf)
Frederick II (Hohenstaufen)
---~60 year break---
Henry VII (Luxembourg)
Louis the Bavarian (House of Wittelsbach, back in Germany)
Charles IV (Luxembourg)
Sigismund (Luxembourg)
Maximilian I (start House of Habsburg, added Burgundy + Netherlands to their possession and was ruling there when appointed HRE)
Charles V (House of Habsburg, Spain!, last actual Holy Roman Emperor)
Ferdinand I (HoH, Austria)
Rudolf II (note: elected successor of Rudolf I, who was German King but not HRE, ruled Austria and Hungary)
+ more House of Habsburg (Austria) and one House of Wittelbach
So we've got a title which bounces between France and Germany (West and East Francia) and Italy, then finally settles itself in the German Kingdom (and it was at least nominally a kingdom then, although they elected their kings) before jumping to Spain and then Austria.
Note, we've contemplated calling Austria "House of Habsburg", which makes them a decent candidate as being the HRE civ.
Further note: King of Italy is hardly as glorious as it sounds, as they never ruled all of Italy, and generally only had authority in northern italy, and usually not even all of it.
Regardless, this clearly isn't a civ, as there were HREs who weren't King of Germany.
Both (the title and the country) gradually lost of importance, mainly because of its "extreme" feudal system, but this isn't the same as saying it was non existant. In fact it became the elective confederation with time, it wasn't born as such.
The German Kingdom was an elective confederation. But they bestowed the title King of Germany, not Holy Roman Emperor. The pope bestowed that, and after Charles V most of them settled for Emperor-Elect and didn't bother to actually be coronated (and were therefore unable to use the title).
The Rathaus represents very well the decentralization of power of this "civ". I doubt one could think of a more appropriate UB. Having the Teutonic Order, France or others in Germany is not desirable, and competing for the title of HRE would make of this mod sort of a EU conversion...
To me, courthouses represent the spreading of a voice of centralized authority and law to the city. The default state is decentralized government. In particular, large decentralized territories are plagued by inability of the nominal central power to exercise authority (such as collecting taxes), which is well represented by higher maintenance costs for not having a courthouse. Germany being a case in point. The local lords are skimming off the top, as it were. A strong centralized authority can crack down on local power and exert central control at a greater distance from the capital (ie, reduced maintenance). I'll note that the Normans spread their domination over England and into Wales at a fantastic rate because of their efficiency (and lots of strong castles) and despite a hostile populace. At least initially they also exerted direct control over local lords and cities (later reduced by such things as the Magna Carta).
About having a bigger map, Europe spans from the Atlantic to the Urals, no more and no less, just because most of us have a western-european-centric education doesn't mean we should focus this scenario mainly on western europe, this is a worldwide forum so I think it won't be hard to find help with eastern europe to make it interesting if need be.
But there's a lot more relevant (to the foundations of industrial europe) action happening at a small scale in Western Europe. You'll note that the small modern countries in Eastern Europe (ie, the Balkans) aren't the areas anyone's actually talking about wanting to add civs. Mostly because those territories were historically controlled by other powers for much of their histories. And northern Eastern Europe tends to feature a larger average country size, with the smaller countries (Latvia/Lithuania/Estonia) either not being important enough to make civs or being bundled in to other civs with whom they've shared a long relationship (Poland-Lithuania). Ie, Important Eastern European civs control (and controlled) larger territories geographically than their western european counterparts. The dominant example of course being Russia who occupied about half of Europe at one point (ie, modern Russia + Ukraine + Belaruss + other former territories) if you count everything back to the Urals.
The only important historical power we don't have represented in central/eastern europe that i'm aware of is the Teutonic Order. (Which could easily morph into Prussia since its in the same location. Or can be treated as a civ in its own right.)
PS: courthouses represent decentralization of power from my point of view. It's a legal authority opened far from the capital. It allows for faster expansion, exactly, which is usually achieved by decentralized empires (and I might add, Empires which grew were forced to gradually decentralize power, of course). Ultimately, it even provides espionage points, definitely in sinergy with what was going on in the HRE.
See above. Decentralized power is the default state. While expansion may be faster, the centralized power (ie, you, the player) doesn't necessarily benefit from it because you have only nominal control over those territories. In CivIV this is represented by your economy tanking.
And internal espionage isn't represented in-game at all. Decentralized authorities have terrible external spy networks because they're spending all their time on internal affairs. Towards the end of the period under consideration (ie, Louis XIV), the best spy network in Western Europe was almost certainly that of France, and it was probably superior to anything in eastern europe too.