Some newer GM's have a hall effect sensor on a battery cable to know how much the battery is accepting, or providing. I hope it would adjust voltage accordingly to faster recharge a depleted battery but I do not know for sure.
I am not sure bypassing the fully charged engine battery will allow any paricular vehicles VR to sense that it is requiring a higher field current to maintain the higher voltage, and thus allow this higher current to be held longer to faster charge a battery.
VR manipulation will be different on every vehicle. I once tried to figure out Why my VR decided to choose 14.9, 14.7, 14.1 or 13.7, and most of the time it was 14.9 or 13.7, very rarely anything other.
I gave up trying to find any logic in its patterns, put a 10 ohm 50 watt resistor in between the two wires that originally went to the field terminals on alternator, thus tricking the engine computer into thinking it was still attached and controlling alternator, and used an adjustable voltage regulator, a Transpo540HD. I modified this VR with an external potentiometer, located on my dashboard next to voltmeters and ammeter, and do the He-man 'I have the POWER' type of battle cry every time I adjust voltage
more details on that modification here:
https://vanlivingforum.com/Thread-Your-Vehicles-voltage-regulator?highlight=voltage+regulator
Basically with this set up, If I have enough rpms available, I can always charge my battery as fast as safely possible anytime my engine is running.
When something else is controlling voltage, that is not possible.
But still, 80 to 100% takes time even at ideal voltages, and 100% regularly is important to battery longevity.
2 years ago my flooded group 31 battery was removed from my van leaving me with only a 90Ah northstar AGM for both house and engine duties. Initially I was planning on another battery for the house, as I am wired for it.
But I found this AGM battery can easily start my engine depleted 65 of its 90AH, and it is highly unlikely I will use more than 65 of its 90AH. This battery now has ~ 575 deep cycles on it, and several hundred more shallower cycles on it, and several thousand engine starts, and turns 4 years old in November.
For the first 8 months of only having one battery, my voltage regulator in engine computer behaved pretty much exactly the same as when I had two batteries, one fully charged engine battery and one house battery at various levels of depletion.
While highly vehicle specific, I can say that on my vehicle, bypassing the engine battery shortly after starting sending all its current into depleted house battery, would not yield any noticeable difference to how long the voltage regulator held a higher voltage, and this is with the voltage regulator inside the engine computer, granted it is a 1989 computer.
And as far as that switching, well I have a 1/2/both off switch. 1 is the engine located battery, 2 is the house battery. i could start the engine on one, then switch to both, then to 2, and completely remove engine battery from the loop, and used to do so, but did not ever notice any different behavior of my engine computers voltage regulator.
But it might have an effect with other vehicles.
Without data it is only speculation.
To the casual reader, Do note that the 1/2/both/off manual switches have a consequence. if switched to OFF with engine running, it can blow the diodes int he alternator, so the direction of rotation of the switch is very important.
AFD is an alternator field disconnect incorporated on some of these switches, which is for externally regulated alternators. One runs the field wires through the switch, so when it is turned to off, it disconnects the field too, saving the alternator diodes.
My switches do not have AFD and if they did I would not run the field wires to where my switches are located anyway.
And i use the term switches, plural, as one switch is for my OEM wiring, switching starter/alternator original battery (+) cable to either battery. My other switches are for loads and charging sources, so I can switch all house loads to either battery or all charging sources like my MEanwell poiwer supply or my solar to either battery. I do not include the alternator in that 'sources' switch though.
But now i only have one battery. All switches are kept in the 2 position as there is no battery currently in my engine compartment, and will not be one until my electrical needs change.