Hi Sia,
In principle, the Match Crystallography filter will eventually match the correct MDF that has been set either in StatsGenerator or calculated from experimental data. The problem is that this process may take a very long time; the Match Crystallography filter operates for a user-set number of iterations, and will terminate after reaching that number even if the actual MDF has not been matched. Matching the ODF is usually quite fast, but matching the MDF can take a large amount of time since the filter optimizes using a Monte Carlo approach, so the likelihood of getting a boundary with the correct misorientation angle and axis is dependent upon selecting two grains next to each other instead of just one in isolation. Because this approach is used, it could take a large number of iterations to reach the desired MDF.
Additionally, using the synthetic builder in this fashion to go after twins will not generally result in twin boundaries that are morphologically flat. To get the morphology correct, the Insert Transformation Phases filter should be used. Try that filter instead for constructing a highly-twinned synthetic structure.
hope that helps,
-Sean