The recently developed refractory multi-principle element alloy (MPEA), AlMo$_{0.5}$NbTa$_{0.5}$TiZr, shows an interesting microstructure with cuboidal precipitates of a disordered phase (${beta}$, bcc) coherently embedded in an ordered phase (${beta}$, B2) matrix, unlike the conventional Ni-based superalloys where the ordered phase (${gamma}$, L12) is the precipitate phase and the disordered phase (${gamma}$, fcc) is the matrix phase. It becomes critical to understand the phase transformation pathway (PTP) leading to this microstructure in order to tailor the microstructure for specific engineering applications. In this study, we first propose a possible PTP leading to the microstructure and employ the phase-field method to simulate microstructural evolution along the PTP. We then explore possible PTPs and materials parameters that lead to an inverted microstructure with the ordered phase being the precipitate phase and the disordered phase being the matrix phase, a microstructure similar to those observed in Ni-based superalloys. We find that in order to maintain the precipitates as highly discrete particles along these PTPs, the volume fraction of the precipitate phase needs to be smaller than that of the matrix phase and the elastic stiffness of the precipitate phase should be higher than that of the matrix phase.