My own cellphone's charging system is a bit of a mess. It has 3 battery fuel gauges, one is totally clueless, second is kinda there, and third is accurate but uncalibrated. The second one is presented to the operating system and the user. There's also a charging circuit (of course), and the battery has its own protection circuit, and additionally the phone has its own low-voltage cutoff circuit which can't be bypassed in programming. Low battery warning comes on at 3.5V, normal shutdown takes place between 3.5 and 3.2, depending on the load and the battery health (some sort of half-arsed attempt at tracking internal resistance, I think). Final "forced" shutdown by software at 3.2Volts. Hardware cutoff at 2.8V, and battery protection circuit somewhere around 2.5V.
As for charging, CC/CV @ 950mA to 4.2V, with 50mA cutoff. The system load is connected in parallell with charger, so if system load exceed 50mA, the charger will never terminate. There's also some parasitic resistance, which means that if system load is 900mA, the battery will end up floating/trickle charging at 4.08 Volt.
I don't know about the thresholds and operations of fuel gauges 1 and 2, but number 3 has a datasheet available. It is a coloumb counter, which keeps track of "learned capacity", and resets its counter to the learned capacity whenever it detects battery full, and from there starts counting down. If it has seen an "undisturbed" cycle from full to empty, it updates learned capacity with the recorded capacity from the discharge cycle. The full threshold is something like: Voltage over 4.05V, charge current >0 and <50mA for more than 10 seconds. The user interface works in mysterious ways, and may indicate battery full long before that, or long after that. And as previously mentioned, the battery charger, if there's any system load, which there always is, will terminate after the fuel gauge detects battery full. If it terminates at all.
Considering all this, I'm not quite sure if there's any point at all in following the instructions in the manual. It would be most useful to charge it full, then use it until empty, to get the initial calibration done, but the manual doesn't mention that. And, if you don't follow it, all you get is incorrect battery meter, which might be annoying and give false impressions about battery performance.