How is Aerion overcoming this problem which is inherent to that configuration?
A few years before the X-3 even flew, a NACA engineer by the name of William Phillips had theorized the possibly of inertial roll coupling, provided precise mathematical equations of the phenomenon, and even devised solutions to the problem if it were ever to occur in practice (which of course it did).
I believe part of the solution is to increase pitch and yaw stability by having a larger tail. Stability augmentation (similar to a yaw damper) can also be used.