Crusader Kings 2, being a game, has to make some sacrifices in order to have a consistent ruleset. As such, it absolutely does not handle titles well in this instance--again, that's not really the game's fault, because it would be impossible to truly replicate feudal inheritances. The big reason for this is that there was never one consistent system across time and place. Their politics were far messier, more personal, and at times ad hoc.

One example is Enguerrand de Coucy, a french baron during the Hundred Year's War. As one of last free barons, directly loyal to the King of France, he was a prominent crown vassal. But because of his marriage to an English noblewoman, he possessed titles in England as well, making him a vassal of the English crown. He was not perceived as a foreign interloper; he was in fact a welcome figure at English court. Even as the two realms waged war, he sat uncomfortably astride the fence for years. Ultimately, he did proclaim his greater loyalty to France, but only out of a sense of duty--there was no particular requirement, custom, or edict forcing his hand.

Of course, at other times this would have been impossible, and at other times still, impossible to say. Again, because its a game, CK2 makes everything clear--borders, loyalty, homage, etc. Realms have clear beginnings and endings. In reality, this was often far from the case. Border counts and barons might proclaim loyalty directly, and then ignore the court for years. Were they independent? There's no clear way to say. A new king might take the throne, and perhaps marcher lords would not explicitly pay homage. Would that be an act of war? Were they declaring independence, or just indifference? Many protocols we now assume to be medieval, like grand coronations, were attempts to resolve these questions. A coronation, an event where the vassals and officers of state gather to pay homage to their new monarch, and receive his own protections in turn, was supposed to make clear who and what the realm was comprised of; we often see them as parties, but for the time, they were more akin to an extremely ornate census.

But like many "ancient" institutions, they have greater roots in the early modern states than actual medieval history. Most medieval coronations were not attended by far-flung counts and barons. Further, for reasons either personal or financial, many kings were not formally enthroned for years--Edgar the Peaceful, of pre-Normal England, delayed his for 15 years.

Power, in most medieval kingdoms, was more akin to a sphere, centered around monarchs or other nobles of prominence, and faded out as it spread into the countryside, than to a clear-cut map with borders and lines and relationship markers. A popular king could expect support from lords that would simply ignore an unpopular king.

All of this is getting away from your question--to bring it back: No, the game does not accurately reflect inheritances across realms. The game cannot, because there were rarely hard-and-fast rules about it, and when there were, they were for specific kingdoms and specific places; Europe as a whole was too diverse to have a consistent set of rules for a 1000-year period.

That said, the "warfare" resolution is probably the least likely scenario, ironically. Exempting a major duchy or crown being "lost" to another realm, a la the 100-Year's War, most minor titles simply weren't worth the cost. Video games wildly overstate the frequency of medieval warfare, which was deadly, enormously expensive, and always involved enormous personal risks on behalf of the belligerents, no matter how high or mighty they were. It was also just plain difficult: It's hard to get a thousand men across the length of Bohemia in a world without airplanes, postal routes, proper roadways, accurate maps, common coinages, language academies, mosquito netting, medicines, supply networks, etc; let alone across the length of Germany in order to force a minor baron to swear homage.

Even the HYW, which was a response to French throne "legally" going to the King of England, was only as long as it was because the will to fight and the capacity to fight were rarely in tune very long. Numerous English invasions were prepared, gathered, financed, and then petered out without ever even crossing the channel. Likewise, many French armies rallied, razed English-loyal areas, and then went home without even a minor battle. With a crown at stake, the war was very low-intensity for literally decades at a time. Lesser titles just weren't worth the effort!