Hiya!! So house names generally are associated with last names, (Habsburg, hollenherzen, etc.). However I think in the case of A Song of Ice and Fire, this is likely a case of Doylism winning out. In the Middle Ages, the idea of a "last name" was not particularly standardized even among the nobility.

Many of the house names we associate with the period are fairly anachronistic, they were attributed by historians after the fact. For example, the French kings are generally referred to as Capetians, but they wouldn't really utilize Capet as a surname, they would be associated with the place or title that a person had, so Louis of France or king of the Franks or king of France. And if we are applying later standards for last names, there would be no changes at all! Let's say that Hugh Capet actually used Capet as a surname. That would mean that every French monarch till the revolution would have the last name Capet. Not only that, but this dynasty was fairly prolific, so the kings of Portugal, the dukes of burgundy, the kind of Sicily, would all have the same last name of Capet using modern standards.

So generally, house names tend to get applied after the fact, the failure of Philip IV's line marks the start of the Valois dynasty, who were agnatic first cousins of the king, but were also count of Valois. This is also helpful because it breaks up periods, specifically the start of the hundred years' war. This happens in English history too, many of the early noble families who started adopting a practice of last names, tended to associate it with a location, such as their original Norman landholding. Even the houses of Lancaster and York as well as the name Plantagenet are somewhat anachronistic. Richard Duke of York is associated with the house of York, but used Plantagenet kind of as a last name to emphasize his male line succession for Geoffrey of anjou, ancestor of the kings of England, who was nicknamed Plantagenet due to a flower he wore in his hat (he was contending with another Plantagenet, Henry VI). We call him Richard of York and his sons yorkists to clarify factions during The Wars of the Roses (medieval nobles had an annoying habit of reusing maybe five first names all the time). Previous kings did not use a last name, they were associated with their title, "king of England."

So the main issue here is more that medieval nobility did not use last names in the same sense that we do, they were associated with a place/title (Habsburg from Habsburg castle in Switzerland) or with their father (Louis son of Charles). If they lasted in to the later or modern period, name conventions changed or historians retrospectively added dynastic names for clarity (Plantagenet, carolingian, Capet, etc.). So I think this more is attributed with trying to make things easier for modern readers, who would not appreciate having to keep track of things like just King Robert, whose brother is Lord Stannis of Dragonstone. Last names did come about later in the period, but not in the same strict sense that we have today. The queen of England's style is likely a marker of tradition, harkening back to the medieval practices of association with place. Hope this helps!!