Many of the same companies are involved in both groups (MMCA and CE-ATA Workgroup), why are there two specifications?
The primary reason for two specifications is that each was formed to serve a slightly different purpose. CE-ATA was formed to be an optimized long-term storage interface for handheld storage devices. ATA on MMC was formed to serve as a way to attach hard drives to the broadest range of existing MMC hosts. This difference in goals has led to different design decisions in each specification.