Using a geometric feedback model of the flagellar axoneme accounting for dynein motor kinetics, we study elastohydrodynamic phase synchronization in a pair of spontaneously beating filaments with waveforms ranging from sperm to cilia and Chlamydomonas. Our computations reveal that both in-phase and anti-phase synchrony can emerge for asymmetric beats while symmetric waveforms go in-phase, and elucidate the mechanism for phase slips due to biochemical noise. Model predictions agree with recent experiments and illuminate the crucial roles of hydrodynamics and mechanochemical feedback in synchronization.