Discordant doping is broadly connoted to atomic substitutions wherein even a marginal amount of incoming atom is unable to adopt the local geometry of the site it occupies and gets inhomogeneously distributed within the crystal. Herein, we report the implication of partial B or Ge doping on the labile, i.e., easily altered, Si atoms of higher manganese silicide (MnSi γ ), prepared by spark plasma sintering of melt-spun ribbons. The synthesized Mn(Si 1−x D x ) γ alloys (where D = B or Ge are dopants) having a Nowotny chimney ladder (NCL) phase, showed a close relation of their structural stability and electrical transport properties to the 14-electron rule. Following the (3 + 1) dimensional superspace approach, the modulation vector component (γ) was accurately determined and correlated with the electrical transport and valence electron count (VEC) of the synthesized samples. Beyond the solubility limit of B/Ge onto the labile [Si] subsystem, a homogeneous formation of Si-rich domains and (Si, Ge) solid solution within the MnSi γ matrix was distinctively observed for B and Ge doping, respectively, which modifies the thermal and electrical transport properties. Comparatively, Ge doping was more favorable than B doping on the Si sites of MnSi γ , wherein the peak thermoelectric figure of merit (zT) ∼ 0.67 (±0.1) at 823 K was obtained for Mn(Si 0.99 Ge 0.01 ) γ , corresponding to ∼50% enhancement, when compared to the Ge-doped HMS single-crystal counterparts.