There has been much speculation since Wonderbolts Academy that Spitfire's VA has been changed since her last appearance. Understandable considering the new and gruff tone she adopted during that episode, but it might just be a case of her putting on a tough act according to some new information.
According to a tweet by Kelly Metzger posted about a month ago, she is the voice of Spitfire on MLP. While she is referring to The Best Night Ever, considering she mentioned that she is Spitfire in the present tense as early as a month ago lends some credence to the claim that she played Spitfire in Sonic Rainboom, Hurricane Fluttershy, and in Wonderbolts Academy. Not definitive proof, but worth speculating on.
Thanks to Whatshisgame for the bit of info.
Link to Tweet in Question
Update: She also did Hurricane Fluttershy, but did not do Sonic Rainboom. The more you know!