Queen of Britain, Empress of India, ruler of places all over the world... I think it makes perfect sense. What other term would you use that could embody world domination and the period in question? (Please say I haven't missed the sarcasm and looked foolish)
No sarcasm at all. I actually have the game and have played it: didn't register it because I didn't find it fun. But the newbie guide I found suggested playing
Brazil for a first game. What does Brazil have to do with Victoria?

The game's about the age of industrialization, not the age of exploration, and almost all the significant colonization's over. There are plenty of other countries as or more interesting than Britain in the period, most obviously the USA, which actually has a significant war to give variety to the economic game. The game also covers WWI: again, what does that have to do with Victoria? And while I don't doubt the game gives the natives more detailed names than "natives", I expect that's pure fluff: for all practical game purposes one native tribe was equally trivial for a European country to conquer as another in this period.
Similarly, in "Crusader Kings" most playable dynasties aren't kings and are going to spend much more time administering their home duchies/counties/earldoms than crusading, and "Rome" includes a lot of playable countries that aren't Roman. The games' titles are designed to indicate the time period. They're not intended to be taken as literally as the title of a figure in a refereed academic journal.
In the EU3 period, on the other hand, native countries actually do things that are interesting in terms of gameplay: the successful ones conquer and expand, they advance technologically, many need diplomacy and most are involved in trade, and sometimes one will fall or fragment. Unlike in Victoria, it would actually add to gameplay to develop them further: they're potentially interesting to play in their own right and some are powerful enough that making them more realistic would make the game more interesting for players of European countries that encounter them.
I don't know where someone got the idea that adding cultures causes a performance hit. Adding country tags causes a performance hit, as countries regularly need to be checked against each other and against every country event in the game, among other things. Cultures and culture groups will just be a few kb of indexed array in RAM that are read from disk when the game is loaded and looked up when the game needs to know about them for some reason. The devs have said that they're trying to remove cultures that don't have country tags associated with them because that causes strange results when rebellions arise, but they've also said that they don't care about cultures that occur strictly in provinces that are colonizable (and therefore cannot have rebellions unless colonized).
As a result of this, adding new cultures in areas that already have one culture for every country, such as Mesoamerica, would be a potential performance issue and a lot of work, because you'd need to add a new country tag, and history, and shield, to make the new culture meaningful. But it's not a big deal at all to add a new culture when you already have several existing countries all associated with one culture, as happens with the "Mali" culture in Africa, or to spread existing cultures over different culture groups.