I'm honestly not at a liberty to talk about a lot of the process, but essentially think of it this way: Yoko Shimomura and Keiji Kawamori were the two main figureheads of the soundtrack remaster. KH2 was virtually all by her (not counting obvious exceptions like Passion etc), while BBS and a lot of the handheld games were a collaboration between Shimomura, Ishimoto and Sekito.
As Ishimoto-san and Sekito-san were not available for the process, updating their tracks would have been a lengthy transcription and build-from-the-ground up process, as compared to Shimomura-san's music of which she still has the scores/audio/etc. At that point I presume that with a finite amount of resources the consensus was to leave the vast majority of BBS as-is.
Given an unlimited amount of time and budget, I think considering the passion poured into this, everyone involved would have liked to do a lot more with the remaster. (This probably applies to all aspects, not just the music) But it is what it is, and everything aside I'm honestly really proud of the result.
p.s. I'm obfuscating and simplifying a lot of it, since honestly as a contractor I can't exactly speak for Square Enix (and a lot of what I do know is NDA), so take my insight as you will. Overall what I can say is everyone involved was and is extremely satisfied with the end product. (Shimomura-san especially was really, really happy with Darkness of the Unknown)