Any battery charger experts out there?
I am not familiar with your particular charger, and previous comments may be correct and what I'm about to say may be wrong for your particular charger, but...
Lead acid batteries use plates with lead on one side and lead oxide on the other. Each cell sees one plate of lead and a second of lead oxide. Considering the electrolyte is sulfuric acid and water, there is an electro-chemical process that takes place.
With a fresh battery, pure lead and lead oxide plates, with a sulfuric acid/water electrolyte, electrons flow freely when an electrical connection is made -- when a load is placed on the battery. As electricity flows, the chemistry of the battery begins to change. The lead and lead oxide plates begin to get a film of lead sulfate. As this film builds with usage, the available energy depletes (battery voltage and capacity drop). When charged, the lead sulfate reverts back into lead and sulfuric acid. That's the concept of the lead acid battery in a nutshell.
In the real world, it takes >15.3 volts to fully desulfate the lead and lead oxide plates. What does an alternator put out? We can argue the tenths of a volt, but it's safe to say in just about all applications, less than 15.3 volts. What this means is that over time, the lead sulfate does not fully revert back into lead and sulfuric acid. In fact, lingering lead sulfate will begin to crystalize. When sufficiently large crystals have formed, they tend to flake off and fall to the bottom of the battery.
Now to your question: A conditioning charge or process is applying in excess of 15.3 volts to the battery to FORCE the desulphation of the plates. Pulsing prevents heat build up, and a "smart" charger will utilize the space between pulses to evaluate progress. I don't know if this helps you in your quest, but is my best answer to your question.