A new electronically non-adiabatic quantum reactive scattering methodology is presented based on a time-independent coupled channel formalism and the adiabatically adjusting principal axis hyperspherical coordinates of T Pack and Parker [J. Chem. Phys. 87, 3888 (1987)]. The methodology computes the full state-to-state scattering matrix for A + B2(v, j) ↔ AB(v', j') + B and A + AB(v, j) → A + AB(v', j') reactions that involve two coupled electronic states which exhibit a conical intersection. The methodology accurately treats all six degrees of freedom relative to the center-of-mass which includes non-zero total angular momentum J and identical particle exchange symmetry. The new methodology is applied to the ultracold hydrogen exchange reaction for which large geometric phase effects have been recently reported [B. K. Kendrick et al., Phys. Rev. Lett. 115, 153201 (2015)]. Rate coefficients for the H/D + HD(v = 4, j = 0) → H/D + HD(v', j') reactions are reported for collision energies between 1 μK and 100 K (total energy ≈1.9 eV). A new diabatic potential energy matrix is developed based on the Boothroyd, Keogh, Martin, and Peterson (BKMP2) and double many body expansion plus single-polynomial (DSP) adiabatic potential energy surfaces for the ground and first excited electronic states of H3, respectively. The rate coefficients computed using the new non-adiabatic methodology and diabatic potential matrix reproduce the recently reported rates that include the geometric phase and are computed using a single adiabatic ground electronic state potential energy surface (BKMP2). The dramatic enhancement and suppression of the ultracold rates due to the geometric phase are confirmed as well as its effects on several shape resonances near 1 K. The results reported here represent the first fully non-adiabatic quantum reactive scattering calculation for an ultracold reaction and validate the importance of the geometric phase on the Wigner threshold behavior.