Here's the deal: The only thing the charger does is provide power to the phone. It has no idea about the state of your phone's battery. Only the phone knows that. The phone has hardware inside that controls how much charging current to provide to the battery. It knows the temperature of the battery. Some even have humidity sensors. If the phone is on (either on standby or in active use*), the charger, or the battery, or both, will power the phone. It doesn't matter!
Here's what I do: When I have power available, I plug it in. When I don't have power available, I use the battery. If the battery gets too low, the phone will go into battery saver mode, and eventually shut down when the battery gets down to 1% or so. And a smart phone knows how best to discharge and to charge the battery, based on the state of charge, temperature and other things. You may even see the battery management strategy improve with software updates. That's why they call them smart phones. They do these things, so you don't have to think about it. Just use your phone, and don't worry about the battery.
*How often do you use the GPS on a long trip, with the phone plugged into the car's USB the whole time? Yeah, the phone gets hot, and the battery charging hardware, along with the phone's software drivers, calculates the proper charging profile to use.
