The Naoto Kubo who orchestrated the FF7 suite with Shota Nakama on the VGO Live at Symphony Hall album is a 2008 alum of Berklee:
https://www.berklee.edu/bt/224/bb_vgo.html.
Naoto Kubo the Nintendo employee says on Facebook that he graduated from Berklee in 2008 and mentions arranging for VGO in a 2011 post.
P.S. here's a Nintendo sound team person with a public Facebook account who knows English and is apparently known by Shota Nakama, someone had better take advantage of this ASAP (Note: I did actually pass this tip on to Chris @ VGMO instead of letting it sit in a thread no one is going to read)