Right - the rogue still hits more often because of high proficiency bonus, combat advantage, targeting NADs with a weapon attack, etc... it did slightly lower the average damage on hit because, for instance, the warlock is using both Cha (18) and Con (14) based attacks, and the person who multiclassed cleric actually took an attack with their Wis 14, but it also slightly improved their chance to hit.
I've no regrets on how it works, but I really wish I knew how to make the character builder use the rule. That's the biggest downside so far.