Recently, a "unified" quantum master equation was derived and shown to be of the Gorini-Kossakowski-Lindblad-Sudarshan form. This equation describes the dynamics of open quantum systems in a manner that forgoes the full secular approximation and retains the impact of coherences between eigenstates close in energy. We implement full counting statistics with the unified quantum master equation to investigate the statistics of energy currents through open quantum systems with nearly degenerate levels. We show that, in general, this equation gives rise to dynamics that satisfy fluctuation symmetry, a sufficient condition for the Second Law of Thermodynamics at the level of average fluxes. For systems with nearly degenerate energy levels, such that coherences build up, the unified equation is simultaneously thermodynamically consistent and more accurate than the fully secular master equation. We exemplify our results for a "V" system facilitating energy transport between two thermal baths at different temperatures. We compare the statistics of steady-state heat currents through this system as predicted by the unified equation to those given by the Redfield equation, which is less approximate but, in general, not thermodynamically consistent. We also compare results to the secular equation, where coherences are entirely abandoned. We find that maintaining coherences between nearly degenerate levels is essential to properly capture the current and its cumulants. On the other hand, the relative fluctuations of the heat current, which embody the thermodynamic uncertainty relation, display inconsequential dependence on quantum coherences.