Conquest: Order 66 won't count?

It's the same reason why DR's Deathmark from his leadership doesn't count toward the Deathmark feat. In Scorch's case, technically the enemy inflicts O66 on themselves. You need to apply it with your own active abilities, meaning you need to hit them three times with CX-2. It is a dumb as bricks clause in my opinion, but it is consistent with what's been done with conquests feats before (the DR Deathmark thing; Caustic Emissions dots don't count towards "inflict dots on enemies" feat because the disk makes the enemy apply dots to themselves, it's not your characters doing it).