I must be missing something and I can be quite dense. Why would you not expect to see higher voltage when charging? Since, voltage drop % stays the same, the higher the charging voltage the higher the voltage will be but at the same %. I also don't see why the voltage drop on the sense wires are a concern.
The SCC is simply compensating for the voltage drop to the batteries and adding more tenths based on that loss. It should be also compensating for temperature if you have a temperature probe.
I am not sure if you have a monitor or not, but I wouldn't be without a good one.
As far as your question, I don't know if generically speaking an MPPT will compensate, or if you have to compensate by setting Absorb and Float voltages "artificially" higher. I would think they would.
MPPT has it place, such as when using 60 or 80 cell panels (higher volts), or when used on-grid.
Bogart Engineering puts it this way: "We have compared at least one commonly used MPPT charger with the SC-2030 and found that under very ordinary conditions the SC-2030 delivered more charge to the batteries. We measured this when the ambient temperature was 70 F degrees in full sun, and when the proper panels matched to the batteries were being used and when charging over 13.0 volts (the most common charging range with lead acid batteries.)
The SC-2030 is a "PWM" (Pulse width modulated) type that is simpler and less costly than a "MPPT" (Maximum Power Point Tracking) type charger. As said, the SC-2030 can give even better performance under some common situations. MPPT technology can give some advantage when temperatures are low, and it is necessary for good power transfer when panel voltage is much higher than the battery system voltage. With the SC-2030 (or other PWM charger), you may be able to get more total performance at the same cost by purchasing another properly matched solar panel instead of a more expensive MPPT solar charger.
A common mistake for evaluating MPPT performance is to compare their (lower) solar input current with (higher) output battery current, and thinking this additional current is solely due to the MPPT charger. This is incorrect, and will give an exaggerated impression of its advantage. A comparison must be done by changing to the PWM controller and then comparing battery currents."
) agrees with this publication and I trust him, since he doesn't have a quota to fill or a hidden agenda.