I have added a new feature to ModelConverterX, it now also uses the visibility tags that are used often in FSX aircraft models. They are read from either the MDL or the X file. And when exporting to FSX MDL they are written as well. So this should mean that such visibility tags no longer get lost when converting a FSX MDL with ModelConverterX.
At the moment there is no way to edit the visibility tags yet, but in the hierarchy viewer you can see which tag is added to a node. I guess for the future I should add some functionality in the preview that allows users to switch the visibility tags on or off.