In the next development release of ModelConverterX you will find support for reading animations from FS2004 scenery MDL files. Or at least a first implementation of this feature. It is working for my test object currently, but I need to look for some more test files to be sure if it is robust enough. So if you try this new feature, please let me know how it worked for you.
While working with the FS2004 scenery MDL files I noticed that there is another problem I have to address. These objects often use conditional display, for example for the scenery complexity setting or for their LOD schema. Currently ModelConverterX does not support these commands yet and thereby they are always assumed to be true. In some cases this seems to lead to objects that appear to be empty because the empty LOD gets loaded only. So I need to figure out how to handle those commands that apply a certain condition.