A spatially 'Mt. Fuji' coupled low-density parity check (LDPC) ensemble is a modified version of the original spatially coupled (SC) LDPC ensemble. Its desirable properties are first observed in experimentally. The decoding error probability in the error floor region over the binary erasure channel (BEC) is theoretically analyzed later. In this paper, as the last piece of the theoretical analysis over the BEC, we analyze the decoding error probability in the waterfall region by modifying the covariance evolution which has been used to analyze the original SC-LDPC ensemble.