The short answer is that the system that is in place for Crusader Kings 3 (and earlier iterations) mostly exists for gameplay reasons and is vastly oversimplified and also applies one set of rules for feudal relationships, where there was almost no such thing in real life. It does not reflect the reality of how the system of noble rankings actually worked, and what they actually meant in practice.

There are a number of issues with how this is presented.

First, the borders of the counties and duchies were not so well defined in the period where the game takes place, and what borders did exist would change as the fortunes of the nobles rose and fell, so they would not be the same from 800-1444 even at the lowest level.

In some situations, the county itself would essentially cease to exist for a time, only to perhaps be resurrected later with different border, and then perhaps disappear again or simply become a titular dignity with no actual control over the area.

One example of this might be when a county or duchy was absorbed into the Crown, either though conquest or something like marriage or inheritance. While there would certainly be some sort of understanding that some places should be assigned as a unit, for the most part, the lands would often be handed out piecemeal to supporters of the King.

A manor here, a castle there. The map of medieval Europe and the subdivisions it had does not look like the neatly bordered regions on the CK3 map except at the highest levels. Most lords ruled a patchwork of holdings spread all throughout the kingdom. They might well have a nucleus of holdings in the area that gave the name to their title, but in some cases, the lord didn't even have their main home in the lands that they took their title from.

CK3 tries to give you a feel for this with the baronies, but the reality is that Kings in this period and other feudal lords tended to hand out lands on the order of a manor here or there at a time, even to high ranking supporters. Assigning large, concentrated areas to lords certainly could happen, but most feudal kings realized that if you hand a lord a concentrated area that they had complete control over, it was basically asking for them to become powerful enough to challenge your power.

Second, it is important to note that while some dukes certainly might have count-level nobles as vassals, both counts and dukes inside a kingdom generally were granted those titles directly by the King, and so while a count might understand that he was of a lower social rank than a duke, he would not consider himself outranked by one in terms of taking directions from them. In most cases it was simply that a duke was just a count who had a much bigger set of lands and some level of prestige.

What mattered to who took commands from whom was strictly based on who the lord of that noble was. If a mere knight was the direct vassal of the King, no duke could order him around unless the duke was placed in an office where they king delegated his authority to the duke to command.

Where the game is interesting is not so much in the sense of dukes having specific counts be under them, but how the system tries to show the tension between the reality of nobles holding lands all over the place, but tradition perhaps making the duke feel that "historically" the counties should be united under him and consequently creating a casus belli to attack the lands of another lord who otherwise had inherited their lands properly.

What the game does is a common feature of popular presentation of feudalism that most people have sort of absorbed. In medieval studies, there are those who take France as sort of the "typical" feudal state and that kind of enforces a situation that didn't exist elsewhere.

France was part of the Carolingian Empire, and as such, Charlemagne had enough power to actually appoint counts (comes in Latin) to specific areas as his representatives. Because this was not a feudal situation, but rather an administrative one, the appointments would be more like what you'd expect: a count managing a territorial county. There would also be special counts called march lords (margraves/marquis) who managed important border areas and dux or dukes which were already a feature of the Frankish polity in that they were the leaders of the tribes of the Franks.

As the Carolingian Empire broke up, of course the period of his rule set the tone as being the most clear set of precedents for how Europe should be divided up. For instance his splitting of his kingdom into the three kingdoms of East Francia (Germany/Holy Roman Empire), West Francia (France) and what was called Lotharingia (Low Countries/Burgundy/Italy) for his sons to inherit actually influenced the map and conflicts of Europe right up until the 20th Century.

Crusader Kings takes that sort of memory of how "things used to be and should be" and uses it for the "de-jure" system in game.

Now, for France this sort of works, even though it is not actually the way it worked even in France itself. Other countries? Not at all.

Take England. England had no duchies in 1066 when it was conquered by William, Duke of Normandy. It only had counties or shires which had ealdormen (who would eventually give rise to the earl title) as local rulers/strongmen under the King. The system of shires and what was called "hundreds" was not at all organized like Carolingian France and it had never been part of Charlemagne's Empire.

William did reorganize England to some extent to introduce the feudal system he was familiar with from France.

However, he recognized how weak it made the French King and he worked hard to ensure that while he was dividing the spoils with his allies, he did not set up strong, centralized holdings for many lords, if any. William worked to ensure that royal authority and justice was accepted everywhere in England in a way that it was not in the France of that time period.

While the Kings of England remained Dukes of Normandy until losing Normandy under King John, they did not appoint anyone as a duke and they did not create any duchies.

In fact, the title of duke is first used for royal princes in England long after the Conquest, and while those princes like John of Gaunt frequently had lots and lots of land and wealth, they were not actually granted parts of the kingdom as duchies.

Only later do non-royals start being appointed dukes, and for the most part, the title was simply just a social prestige ranking for purposes of precedence that was granted to those who were already nobles. It never had any effect of placing earls under the dukes.

And if England and France were barely anything like what CK3 shows, the rest of Europe is even further. The Holy Roman Empire certainly had its dukes and counts and margraves, but it ended up with so many special divisions and special areas that were immediately subject to the Emperor that what really ended up structuring the Empire was not dukes and counts as much as the Elector Princes (who sometimes happened to also have a ducal title) and their domains.

Finally, places like Italy and Eastern Europe had their own lordship concepts and politics around them. Once feudalism did make it to those areas, it often only resembled what it looked like in Western Europe in broad outlines.

So the answer to your question is that while there were certainly counts and dukes with territorial rulership, the use of those titles as simply titles started almost from the beginning.

One other thing I should point out before I close. As pointed out above, titles duke and count come from the Latin dux and comes and those were titles from the late Roman Empire. While generally a dux was of greater stature than a comes, and sometimes a comes was subordinated to a dux, the fact is that really they are just two titles that mean leader or companion. Even the Romans did not enforce a strong hierarchy putting a comes under a dux and they did not always use the titles to mean the same thing consistently.

When the "barbarians" took over the Western Roman Empire, they absorbed the titles but they didn't really apply them the same way that the Romans did. Much like you might see some petty strongman in a post-apocalyptic movie calling himself the King of Brooklyn or something, those who called themselves dux or comes or patrician after the fall of the Empire probably took what whatever titles that they could force others to recognize or at least accept. That means that there was never a strong acceptance that a count would actually work for a duke unless specifically assigned to the duke, even from the beginning.