That's the way it's not only written, but spoken in Japanese.
Imperial / kōki which counts from alleged founding of Japan in 660BC
Era / nengō which counts the years from the start of the Emperor's reign
European / seireki adopting the International standard date counting from the alleged birth date of Jesus Christ
Today is 平成23年5月13日 of Mikado Heisei, the 125th Emperor of Japan
Kōki is not used by anyone with a straight face in this day and age.
"Mikado Heisei" is an extremely uncommon way to refer to the emperor. "帝平成" gets 724 hits on Google, and "Mikado Heisei" gets 6, in 5 different languages---the first of which is your post above. Even the Japanese-language wikipedia page on him doesn't use the word "帝" anywhere.