I suppose they're not violating that, since apps aren't distributing the font file.

To whatever degree that apples to San Francisco, does it not also apply to Apple Color Emoji.ttc though?

Or does the "font shapes not copyrightable" rule not apply to fonts that have more to them than monochrome shapes?

It's Apple's playground and they can enforce whatever idiotic rules they want, but I don't see how using their emoji font is any different from any other font they provide. IP rules aren't a justification for it.

All the justification they need is "We're in charge and we reserve the right to be arbitrary and capricious with app approval," but that doesn't mean I like it.

If you render the shapes to a bitmap, you own the compete copyright to that bitmap.