It's obvious that Sonic Team doesn't really "exist" anymore, videos of PSO2 being made in the Sonic Team office (with the Sonic plushies) make it obvious.
Rythm Thief is technically also a Sonic Team game, being directed by Shun Nakamura. Now only Sonic games have the "Sonic Team" name on it, for whatever ridiciolus marketing reason.
Could it be, that the same thing happened to AM2? Only on After Burner Climax and VF5 you see the AM2 logo anymore. But they have made other games, from the Lindbergh catalouge on...
To me it seems like AM1, AM2 and AM3 just blended in together.
Why is it said that AM2, are working on Border Break? Could easily be AM3 staff, since they made Virtual-On.