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The alicorns on the flag represent the combined strength of Earth, Unicorn, and Pegasus, of which is the founding principle of Equestria. They are not meant to be Celestia and Luna. Spike even says that this takes place before Celestia. The fact that Celestia and Luna are alicorns is likely a genetic thing (because the species CAN inter-breed, Rarity's dad was an earth pony), and so it was just a coincidence that there were eventually ponies born that looked like the ones in the flag.