Federation Commander

As long as you declair that you are intending to hit weapons or power before rolling to hit, does burn through still use that set of rules or does it become random.

The burn-through damage does get treated as directed. So you'll have a higher chance of hitting what you want. It's a good way to strip some phasers off a ship at long range.

The giant robot is correct. If so declared before rolling, burn-through will use directed targetting.