Its exactly as you say.its lowering cd instead of resetting it completely (killing intent and red lotus secret). Akatsuki orochimaru lowers Itachi's bond cooldown the same way as normal mysteries of others, jonin must be working the same way.

Wanna know what else is unfair about his mystery? While jonin minato's mystery interrupt+tag effect gets extended from 2 targets to whole team (+30%dmg and paralysis as bonus), itachi's buff removal doesnt work the same way- even though it hits whole team, it removes buffs on only targetted ninja. While reset isnt such a big problem, since itachi is more suited as a backline support than pos1 material, not being able to remove team's buffs seems like a wasted potential. Maybe it was intended, as he was given away for free (and team buff removal would be really strong), where jonin is event ninja which you actually have to buy.