I figured out that you can use the following to get all the parameters of the Kalman Filter including the augmented model used by the observer:
>> [L, M, A, Cm, Bu, Bv, Dvm] = getEstimator(mpcobj);
>> Cm * out.X_EST(end, :)'
Can I get this Cm matrix in simulink so I can calculate the output estimates during the simulation?
I couldn't find a way so I used a from-workspace block to get the precalculated Cm matrix and used it to copmute the output estimates like this. If anyone knows a simpler way, please let me know!