The paper starts by presenting a new concept of differentiation similarity transformations for commensurate pseudo-states-space representations. It is proven that a pseudo state-space representation with a commensurate differentiation order and a dimension of the transition matrix n can be similar to a pseudo-state-space representation with a commensurate order υ and a dimension of the transition matrix kn, where k is an integral number. A direct consequence of the aforementioned concept in fractional subspace-based identification methods for MIMO systems is that an overestimated pseudo-state-space representation has multiple minimums at commensurate differentiation orders over the integral number k. This result is especially visible when deterministic input/output signals are considered and less visible in the stochastic case due to overestimation.