The reason why the internal faces do not work any more is by desing.
After some problems with internal faces after the neighbouring parts are merged (in PrePoMax, only parts can be hidden, so after merger, the internal faces can not be reselected by the user or automatically), I decided that keeping internal faces which cannot be used later is not useful. And it is also topologically incorrect.
So this will stay as it is. However, I also see the need to be able to organise items in the tree, so I will look into adding support for moving and grouping tree items. In this way, the problem you describe can be solved in a correct way. It will introduce some additional work, but it will bring a better user experience for the future.