@hironakamura
According to that Rainbow ~ Twilight episode that they teach the new recruits in the place of Spitfire, Twilight in her lecture stated that Princess Celestia officially created the Wonderbolts after being amazed by the flying skill of a specific group of pegasi of the Royal Guard, thereafter I think it is safe to say the Wonderbolts are a branch of the Royal Guard, the elite air force of the Royal Guard if you wish and yes every Wonderbolt officer is considered to be military personal including Rainbow herself.
When Tyrek attacked Cloudsdale it was the Wonderbolts who tried to engage him instead of the Royal Guard so it also is likely they are the “police enforcement” of Cloudsdale.
If you think about it Captain seems to be the highest military rank in Equestria’s military, officially we have Shining Armor as the Royal Guard captain and Spitfire as Wonderbolts captain, they’re likely to be in the same hierarchy patent, both answer directly to the Princesses as well.
So by theory Princess Twilight could order Spitfire to assemble a team for a mission which would be damn cool to see.