The damage increases in one additional step over time while locked on to a target, making the Void Ray much more effective against units it can focus on for a long period. Deals 20% extra damage to Massive units. All Massive units are also Armored, so both bonuses apply, and the table above includes both bonuses.
There is also a visual indicator for what level the damage is currently at: at each of the two steps/charges another energy spike joins the beam, making it larger. The charge level does not go back down to the initial amount until a few seconds after firing, so if you switch targets quickly you will keep the current charge. The damage only changes at the second charge, but this does mean that it's possible to get the extra damage either by attacking a single target for 12 seconds, or attacking one target for between 6 and 12 seconds, and then another target for at least 6 seconds.