I don't think it's that clear that one thing follows immediately from the other. They allude to future events, but for example, Togami isn't with Makoto here even though they were together at the time of the DR2 epilogue. If 2 or 3 years passed between those two games and the beginning of this season, they could easily use "growth spurt" to justify why she'd somehow be significantly older looking now.
I really doubt it would take two or three years for them to give Makoto a trial given that they knew he took them already. It's probably been like a month or two at best since DR2 and maybe about a year since DRAE. Ignoring that, Miaya is the leader of division of the Future Foundation so she's had to have had significant contact with others, she'd have to had this appearance for sometime before DRAE even started.