hard to tell if they "liked" the PC form factor more, or if it was because they intended to have ISA slots, or simply because they had the casework already designed for the never released CBM 900 Unix machine.
I have a feeling it was the ISA reason, because of the intended bridgeboard replacing the Sidecar and need for ISA slots it made sense to conform the Amigas sots to the same form made all the easier because Commodore never really released any ZorroI stuff. The intent to have ISA likely dictated the ability to use the existing 900 case more than the 900 case dictating the Zorro II change.