Voltage and current measurement of battery Single ended or differential?
I think all your proposed solutions are possible good solutions.

If implemented  properly I think it does not matter that much if you go for a full differential or partly single-ended solution. But in general differential circuits are less sensitive to external disturbances.

Do make sure that the (differential) amplifiers have the right voltage gain such that you will be using the ADC's full range.

Another potential issue, since you will be using a switching converter, there will be switching noise on the measured current and voltage. Using a low-pass filter between the shunt resistor/ battery and amplifier input might be sufficient to suppress this noise enough. Some averaging of the measured values from the ADC might also help and improve accuracy.

And kudo's for doing your homework and you already know a lot more than many answer-seekers on this forum ! :-)