Recent work of Cesana, Craig and the third author shows that the trace of plane partitions is asymptotically equidistributed in residue classes mod $b$. Applying a technique of the first two authors and Garnowski, we prove asymptotic formulas for the secondary terms in this equidistribution, which are controlled by certain complex numbers generated by a twisted MacMahon-type product. We further carry out a similar analysis for a statistic related to plane overpartitions.