The triple-phase shift (TPS) modulation for the three-phase dual-active bridge (DAB3) extends the feasible range of soft-switching operation in light-load conditions, compared to the single-phase shift (SPS) modulation. This paper proposes generalized instantaneous dual flux control (GIDFC), which is capable of handling not only SPS modulation but also TPS modulation with optimized dynamic performance. Voltage phase difference under SPS or TPS modulation is interpreted as a phase difference between the fluxes on both sides. By regulating the fluxes into hexagonal or triangular trajectories with the desired phase shift, the SPS or TPS modulation can be achieved, respectively. By incorporating the optimal load-angle transition method, GIDFC demonstrates optimized dynamic performance with seamless transitions between SPS and TPS modulations. GIDFC is validated through simulations and experimental tests.