What the note probably refers to, if the
regulator and a
solar controller are both connected to a
battery, and they are not programmed correctly, it can happen that the alternator regulator "sees" the solar
charger voltage and thinks the
battery is charged, turning off.
Also, the manual describes a minimum bulk time and a minimum absorption time. After that time,
charging will momentarily stop while the regulator checks battery voltage and calculates the remaining needed time, or switches to the next phase. So that might have been witnessed.
An
overheating alternator, or hot
batteries, if such temperature sensors are connected can cause reduced output that could be interpreted as the regulator cycling off and on.
I suggest following the manual to load the default program for your battery type, then test by itself without any other charge sources. You might find it works fine. From there adjust it for your needs, if the default program isn't adequate.