The dude does sound like an experimental subject where they're designed to have multiple personalities, enabling them to turn on the "terrorist" mode on and off, while no amount of probing by officials and government would be able to link them back to the organisation.

However, "programing" artificial personalities may be hard, if not impossible, so after they train them up as a terrorist, you simply wipe them and let the other develop naturally, calling them up only when needed. Since it's "natural", nothing should seem suspicious to an outsider neither. After all, you can't screw up an act if you're not acting.

Interesting, and while I haven't seen Honey and Clover, the characters still have a really nostalgic feel to them.