Did just try for myself against test dummy niporailem.It doesn't negate the negative penalty from the focus gem, but it helps minimize the effect.
Used a diamond mace ,100 di + undead slayer + perfection nearly negates malus.
The same + eoo do completly negate it.
Not a single hit above 300 di cap, weapon specials didnt change that. Im still a bit confused about that, as i remember a statement from logrus that you can go above cap, but my own tests did never show that.
Maybe focus gems stack only with lumberjacking bonus?