The motor (as a generator) can only deliver power to the battery if its terminal voltage exceeds the battery voltage.
The page you reference skips over a lot of detail, but in section 4, the author is actually using Q2, D2 and La (the inductance of the armature) as a boost (switching) converter to raise the voltage sufficiently to charge the battery.
Note that the situation in section 6 is different. Here, he seems to be ignoring the armature inductance and simply applying reverse voltage across the motor to slow it down more quickly. This does not result in any regeneration, since no energy is actually returned to the battery. It is possible to do regeneration with a full bridge, but it's more complex than what is shown there.