PWM works by shorting panels to the battery in bulk phase and can't regulate current directly in that mode.
Once absorption is reached, the controller begins rapidly (hundreds/thousands of times a second) connecting/disconnecting the panel from the battery. This effectively regulates both the voltage and current to maintain constant voltage and reduced current - this is basically how any non-MPPT charger works.
Remember batteries are loads to chargers, and they DRAW the current. Additionally, current flows because of a voltage difference; however, this difference is always very small. Lastly, a voltage drop only exists because current is flowing through resistance. If no current is flowing, there is no voltage drop. If only half the amount of current is flowing, only the voltage drop will be half.
The scenario you describe will cause the current to reduce simply from the voltage drop. This reduced current will reduce the voltage drop, thus permitting some amount of current to flow. No intelligence on the part of the charger is required. The charger will continue to see 14.4V at its terminals while the current naturally drops as the voltage naturally rises. This may dramatically increase the charge time.
