Kelly Metzger voiced Spitfire in Hurricane Fluttershy, Best Night Ever, and Wonderbolts Academy, it looks like Nicole Oliver was the one to do it in Sonic Rainboom. That would explain the variation in vocals for the pony. Mystery solved! Based on this track record, it looks like Kelly is the official VA from here on out, assuming we see more Spitfire in the future.
Thanks to HotCocoa for the heads up!