Quite simply, Apple Color Emoji isn’t licensed. They could have chosen one of the free emoji fonts like Noto Emoji, or if they don’t like any of the existing free ones, commission their own. Instead they chose to adapt an unlicensed proprietary font.

> This is a puzzling move on Apple’s behalf…

Hardly puzzling. What’s puzzling is their developers and designers seem to have never heard of licenses on artwork. And no, “your emojis are boring and we’re making them awesome” is not a valid copyright infringement defense.