Hikaru never once in the tv series flew a VF-1A. According to flight tests, simulations etc, the more skilled the pilot is, the more "privlages" one shall have. Since Hikaru has won many flight competitions not to mention maybe just MAYBE Roy putting in a good word for him got him to be a top knotch pilot.
There is a scene where he has an unpainted VF-1J during his training shooting at stuff, never do you see him piloting a VF-1A unless it's animation error when an episode's animation turned, "Crappy" cause if so, than you can say even Roy piloted a VF-1A in the series...
The J variant was also discussed as being a Jr Officers fighter, those with high skills and great potential. Now before you say, "But what about max?" I believe max even states he was very inexperinced and later when he got use to the flow of battle he became some what of a genius. You never hear how he actually did during all those tests he took, nor if he had any prior experince before signing up with the UN Spacy forces...unlike Hikaru.
I suggest you go whatch episode 6 Daedulus Attack again. There's no animation mistake there. Hikaru is clearly shown piloting a CF-1A landing on the Promethueus. This is right before the animation of Hikaru landing from gerwalk changing into battroid while piloting a CF-1J.
Maybe those scenes signifies that Hikaru was progressing in his training so he was promoted to fly the 1J.