This seemed the most likely consideration to me as well, but what I find odd about it is that sequencing in the games' native soundfont from the get-go, as the track is being composed, would involve less work. One justification could be that writing with custom instruments first is less creatively restraining, but that was never really a problem before.
It would disappoint me if Masuda's only contribution was sort of a loose melodic foundation, but the tracks still stylistically bear his "mark" so at present I have no way of confidently asserting what the full story is.That said, the track list for the B2W2 score mentions that the "Gym Leader's Final Pokemon" theme was "composed" by both Masuda & Ichinose, so it's probably safe to assume that Ichinose added in that gorgeous second stanza (not to mention it very much resembles the climax of his Frontier Brain battle tune from Emerald). The World Champion theme's composition is entirely Masuda's though so I hope that unique key progression at the beginning was his!
I kept thinking Colress' battle theme was Sato, but yeah, incorporating the event theme motif into the battle theme is something they've done a few times before.
I should probably speak a bit about the X/Y soundtrack. Adachi is far more versatile than I've given her credit for in the past; Route 8, Cyllage City, Dendemille Town, the Gate theme, and even that unsettling riff that plays when Lysandre makes his sporadic story appearances ("Dark Skies") are all among my favorites. She, like Morikazu Aoki, is immensely capable when given more time in the spotlight. I found Kageyama's Routes 2 and 4 charming as well, with 18 being a late-game stunner. It's a shame Ichinose is MIA, but even without him I thought the score surpassed the previous two generations, barring the more tepid lineup of battle themes. Actually, what I fear most is that Masuda will stop composing battle music altogether (he's already winding down), and we'll be left with themes that come across as shallow imitations. That said, the other members of the sound team shouldn't be afraid to break their own ground if it comes to Masuda forgoing his musical duties altogether. Kageyama's "Super Training" and "It's a Pokemon Battle!" tracks could actually fill in the traditional battle theme style better than the Rival battle theme for instance. The Super Training music actually reminds me of this cool thing from about 0:42 onward, which I already thought bore a faint resemblance to older battle themes' sensibilities.
