I always thought they'd just stick with Makoto Yuki for both since it's a gender-neutral name, but I guess this makes life easier since Persona already has 2 Makotos (Persona 3's Yuki & Persona 5's Nijima). That plus this was a nice way to throw manga fans a bone (as Makoto Yuki's manga name was Minato Arisato). For reference, this is Minako.
Source: SEGA Heroes Character Request Survey