Art Imitating Life
He noted there was "a Water Gym every Gen."
Second didn't have its own water gym. Or, to be more precise, Johto doesn't - the revisit to Kanto involves (with one exception, Blaine) the same gyms with (with one exception, Blue) the same types and (with two exceptions, Blue and Janine) the same leaders.
Yes, it can be argued that Koga and Janine should count as different leaders - but Lenora and Cheren are even more different, in that they have different gyms at different positions in the order (second and first respectively.)
Yet Lenora and Cheren are not being counted as separate normal-type leaders, or else we'd have four (with Whitney and Norman.)
Nor are Drayden and Iris counted separately (the one you fight depends on what game you're playing,) but the brothers are (the one you fight is effective vs. your starter.)