What I mean is that I know a charge controller regulates the voltage and current into your batteries to protect them (and CC's can incorporate MPPT's to extract more from your solar panels), but do the MPPT CC's take ALL the energy you could generate from the PV panels and put all of that energy in the batteries (neglecting efficiency here because that is irrelevant for the purpose of this question)? Or do they also tone down the rate at which the batteries get charged as they get close to maximum capacity (I know the CC will stop charging the battery once it reaches full capacity).
For example, would the below be something that could happen?
A theoretical PV system could generate 12 watts with an MPPT CC at a given moment in time. If the batteries were at 5% charge, they could accept a charging rate of 12 watts, BUT since the batteries are at 75% charge, they can only be charged at a rate of 7 watts, so the MPPT CC sets the PV panels at 7 watts, thus losing you 5 watts from your PV panels.