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The choice of the electronic representation in on-the-fly quantum dynamics is crucial. The adiabatic representation is appealing since adiabatic states are readily available from quantum chemistry packages. The nuclear wavepackets are then expanded in a basis of Gaussian functions, which follow trajectories to explore the potential energy surfaces and approximate the potential using a local expansion of the adiabatic quantities. Nevertheless, the adiabatic representation is plagued with severe limitations when conical intersections are involved: the diagonal Born-Oppenheimer corrections (DBOCs) are non-integrable, and the geometric phase effect on the nuclear wavepackets cannot be accounted for unless a model is available. To circumvent these difficulties, the moving crude adiabatic (MCA) representation was proposed and successfully tested in low energy dynamics where the wavepacket skirts the conical intersection. We assess the MCA representation in the case of non-adiabatic transitions through conical intersections. First, we show that using a Gaussian basis in the adiabatic representation indeed exhibits the aforementioned difficulties with a special emphasis on the possibility to regularize the DBOC terms. Then, we show that MCA is indeed able to properly model non-adiabatic transitions. Tests are done on linear vibronic coupling models for the bis(methylene) adamantyl cation and the butatriene cation.