I think the answer to this question is the way the MATLAB block is implemented. In the traditional CIC decimator algorithm, the delay unit in the integrator is used in the feedback path, but in the MATLAB block it uses the unit delay in the feedforward path of the integrators:
Although the filter will be equivalent (same frequency response), the numerical output of the two implementations are a different (the mirrored look that I mentioned in my question).
I don't know if there is any way of implementing the CIC in Matlab using the unit delay in the feedback.