Why is Royal Flush ever listed separately from Straight Flush?

In modern times (since 1980), this is likely because a Royal Flush pays substantially higher in video poker than a Straight Flush. While payouts vary by machine, it's common for a Royal Flush to pay 800 - 1000 times the stake, where a (non-royal) Straight Flush only pays in 40 - 90 times the stake.

For player-on-player poker variants, a Royal Flush is not actually a different hand category from a Straight Flush, and many hand ranking lists (such as Wikipedia's) do not list it separately.

Poker is full of slang; there are an especially high number of poker terms for various "best hands". The best hand possible in a particular situation (such as given a set of community cards) is kowns as "the nuts". A pair of aces as hole cards in Texas Hold'em is the statistically best pre-flop hand, and so has a whole pile of nicknames (Rockets, American Airlines, Bullets, etc.). An Ace through 5 straight is the best hand in some variants of lowball poker, and so has picked up the nickname the "Wheel". Naturally, poker has a nickname for the best hand in the game as well, i.e. the Royal Flush.

Merriam-Webster lists the term Royal Flush as originating around 1868, but doesn't list a source. However, it is worth noting that the term "Royal Flush" is prevalent enough to have made it into Merriam-Webster, where terms like "wheel" or "rockets" are not. Given this, I would speculate that some hand orderings list Royal Flush as a separate hand category from a Straight Flush to prevent confusion on behalf of the players who are aware of the Royal Flush as a poker hand (and thus expecting it to be listed in a hand ordering).

I would think this has something to do with the fact that a straight flush has multiple card combinations per suit to achieve it, making it more common (2, 3, 4, 5, 6/ 8, 9, 10, J, Q etc...) and the Royal Flush only has one card combination per suit (A, K, Q, J, 10).

The Royal Flush could be a straight flush also in theory, (I understand this is where your confusion lies) but the fact it has all of the Royalty cards in it, makes it a one of a kind "straight flush" in the suit. It also stands to reason that it is a lot more valuable of a hand than a normal straight flush as it has all of the highest value cards in it.

The only real supporting evidence for the origin of the name Royal Flush is literally only in the dictionary. It states that a Royal Flush is made up of the top 5 "honors" of any suit. To me the word Honor further suggests Royalty. The fact that Royal figures (King and Queen) are in the line up of a Royal Flush is the best suggested evidence of its origin.

There are a number of different hands that have a specific name. For example, A-2-3-4-5 is called a Wheel. The Royal Flush obviously gets its name from being the highest hand, and specifically having royalty in it (although one could argue so does a King high.)

As for the mistake of ranking of Straight Flush being lower than 4 of a kind, this is easily dispelled by looking at the math behind them. There exist only 40 straight flushes (of which 4 are Royal) and there are 624 unique hands that rank as four-of-a-kind.

One reason for it persisting would be in Video Poker where a Royal Flush tends to pay out significantly higher than the other Straight Flushes. This doesn't answer the question about how it managed to still exist before Video Poker was around, though.

I have had it conveyed to me recently that it's listed separately potentially due to wild-cards and how they affect the math - that perhaps a straight flush is not as difficult to acquire anymore where a Royal flush is. However I have not had an opportunity to run the math on it. I would welcome an addendum if someone does.