Oh shit. I started making some Japanese searches to see if I could find anymore info on which Pokemon were designed by who. And I found some really big info.
Atsuko Nishida didn't design Eevee, Flareon, and Jolteon. Nishida talked to some fans on Twitter exactly a year ago, and she clarified that she only designed Vaporeon and all the later evolutions. Eevee, Flareon, and Jolteon were designed by Motofumi Fujiwara.
https://twitter.com/atsuko_nishida/status/783643367523557376