Serial vs Parallel Thoughts
Using 2x24V panels for 12V charging yields the exact same power input to the controller so I would not expect any difference based on the panels, ie the voltage is not less in the early morning. So twice the voltage or twice the amps. Wiring is different and a given MPPT controller could have different efficiencies depenting on the input voltage or amps.
For 2x12V panels for 12V charging could use a PWM controller for parallel and a MPPT controller for serial which involves wiring and controller differences. It also involves temperature differences and could favor either one. With morning temperatues above or below 77F (STC) as the panel output can favor one or the other. If the same MPPT controller is used for serial vs parallel then likely the same except for wiring and efficiency.
Just my 2 cents. I don’t recall seeing in testing on this subject.
