Nope. The MPPT doesn't try to optimize a single panel or a single string, etc. It simply tries to optimize a source.
The combiner box is just placing the array into one big Vmp & Imp - basically the equivalent to one large panel.
The efficiency losses would come in component variation. Many panels have ±1-3% ratings, with variations in both voltage and current, so even the same brand and model may perform differently in both voltage and current. The lower voltage panels would adversely impact higher voltage panels while the lower current panels would force the higher current panels in series to run at the lower current.
Example panel:
300W
30Vmp
10Imp
3S3P would simply look like one big 90Vmp, 30Imp panel to the MPPT, and it would try to find the max power point.