Why is Royal Flush ever listed separately from Straight Flush?
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.