That's just Apple being typically arrogant (and other font designers following them, sadly).
The way to write a flag in emoji is to combine the two letters of its country code; e.g. for the French flag you write REGIONAL INDICATOR F + REGIONAL INDICATOR R. The font then magically turns that two-character sequence into a single glyph.
An emoji font could include up to 676 (26*26) flags; I think WhatsApp has something like 45 flags already (on Android).
My understanding is that Apple just included the standard Japanese emoji set, to help sell iPhones in japan. For a long time they were even hidden on non-Japanese iPhones.
The standard Japanese emoji set is pretty randomly put together and I don't remember my old keitai having that many country flags.
I think you mean: 🆒
Though admittedly that shows up as a blank for me :( This one works for me though: 😃
So font makers, please add all emoji to unicode fonts? Thanks!
Also, why do Emoji have flags for 10 countries but not for all the rest?