Funny enough, there's nothing in there saying Move-by-Wire is not subject to the augmented maximum of +4 direct bonus to initiative, so in theory, it would cap and you wouldn't get the full +6 or +9, but that's obviously not rules as intended.
However, per the book, the bonuses are as follows.
Rating 1: +1 Reaction, +3 Initiative.
Rating 2: +2 Reaction, +6 Initiative, +1d6 Initiative.
Rating 3: +3 Reaction, +9 Initiative, +1d6 Initiative.
You don't get a second die that way.
That said, the move-by-wire system is only incompatible with other augmentations that boost reaction. You can still use spells and chems. Jazz will give you +2d6, and if your mage can manage two hits on your essence 0.04 butt, you can get that last die for 5d6, with Reaction at your augmented maximum. You wouldn't get above +9 direct to initiative, though, because you're already above the augmented maximum. Cerebellum Booster, though, would let you squeak out just a little bit more by boosting Intuition.
