I think there are a number of reasons why a dragon atop Gringotts might make sense. The Wizarding World is a timeless (i.e. set in no particular moment from the series) hodgepodge of iconic events, characters, and places in the wizarding world, and Potter fans are already in a position of having to disregard a certain amount of thematic discontinuity, anachronism, or outright error...
Also, since they had originally intended to include a fire-breathing dragon in Forbidden Journey but had to cancel it at the last minute, this is their opportunity to impress guests with that technology...
...Either way, I imagine they're gambling that the special effects will win over even hardcore HP fans, in spite of the anachronism/discontinuity.