The Booster Charges seem to be using only flat auto-attack damage for their calculation. The tooltip is worded in the same way as, for example, Storm Blade, as a percentage of weapon damage. But Storm Blade's damage clearly does more per weapon dps, probably because it includes attack power.

Sweet mentioned that Trion would like the new Charge Booster to incentivize deeper investment in the Sab tree. If the Booster Charge damage is calculated only from auto attack damage, there is still scant reason to give up the points in other trees.