I remember someone in the staff mentioned this (buuuut I forgot who, sob, I follow a couple of animators on twitter), but it was backwards-adapted from that anime episode due to its popularity!
Basically, Ditto used to transform pretty much perfectly. Then, there was that anime episode you mentioned with Duplica's first problem Ditto (her second problem Ditto shows up in Johto and transforms while staying Ditto-sized!).
It's just that Ditto-faced transformations were so cute, they started being included in merchandise...
https://bulbapedia.bulbagarden.net/wiki/Ditto_Collection
... and I guess it became a new standard, and after being backwards adapted from the anime to game-based merch/the rest of the franchise, it was re-adapted from there into the Sun & Moon anime, just because it's so popular and CUTE.
It also helps to make transformed or disguised characters clear to the child audience--just like how Team Rocket's disguises are easy for the viewers to see through (so we still know who we're looking at 99% of the time), while in-universe, they're not supposed to be THAT easy to recognize (except when... they are... in that case, it's just everybody having a less-than-brilliant moment)... you see the same stuff in other kid's media, like 90's Sailor Moon (Zoisite and Venus' Sailor Moon disguises were treated as VERY CONVINCING in-universe, but...
Zoisite has such small, green eyes and
Venus/Minako's hair is SO POOFY and short compared to Sailor Moon's long and flat-lying hair!).