Transfer Active Morphs isn't going to be perfect, it is after all an automated process. If the clothing mesh is lower resolution than the figure, for example, a morph may move a vertex out where there's nothing to move in the clothing and that will cause poke-through (it can't think to bridge from elsewhere). Another tool you can use that may help is Collision - select the clothing item and (from memory) go to Create>New Smoothing Modifier; under the new Mesh Smoothing group in Parameters set the Collision target to Victoria 4 if it isn't and if necessary make small adjustments to the iterations. You can also add a Push Modifier, again in the Create menu, which is similar in effect to an expand all morph.