The British modelled it after their own markings when they formed the Royal Indian Air Force. They just changed the blue, white and red of the Union Jack to the safron, white and green of the then British Indian Flag. After independence the Indian Air Force kept on with it.
British Spitfire,
Royal Indian Spitfire,
British Hawker Hurricane,
Royal Indian Hawker Hurricane,
There's nothing wrong with it though. The tail markings don't necessarily need to be your flag or a flag at all. For example,
Croatia just has its coat of arms
Poland,
Greece,
USAF has codes which denote the unit the aircraft belongs to,
http://www.military.cz/usa/air/air_accessories/usaf_tail_cod/usaf_tail_cod.htm
Even the PAF didn't have the complete flag for a very long time,