>>58257555The girl that Sugimori drew was, by his own admission, something to fill a space. The original female protagonist of Gen I in concept art and sprites was an edit of Red's overworld sprite, it's the same character from the Capsule Monsters art. The Special manga decided to use her to represent Blue, which had already been released in Japan, and an origami book used her too. Sugimori used her as the basis for the FRLG protagonist (who did not have an official name at the time). Fans called her Leaf because that was an internal option in FRLG, though Red could similarly be called Fire. LGPE adapted the same design as a character called Blue, but Masters and merchandise all went with Leaf which had become standardized in the fandom. The same thing happened with Silver and Kris.
Whether or not Leaf and Blue are the same character is just splitting hairs. Leaf was a mostly blank slate prior to Masters, so Blue being the way she was didn't really matter. With Masters, Leaf was given a distinct personality and definitive name, but they're still the same idea.