The characters having different heights in the West predates DRV3. Though, most of the time the ultimates were accidentally made shorter. Like Hajime's 179cm in the original, but 5'8", which is around 172cm, in the Western release. Nagito, similarly is a single centimeter taller than Hajime, but he's 5'9", which is around 174cm. Both of them should be 5'10-11 or so. Peko is 172cm in Japan, but 5'6" (closer to 168cm) in the West. I checked the wiki real quick, and Angie was also made shorter, being 157cm vs 5'1"(155cm).
Kaede being taller is kinda odd, yeah.