First you need to make sure that on runtime import the hierarchy option is to keep full hierarchy and prevent datastmith to bundle all in one actor ( I think you are already doing that).
Second, correct my method will export full level if you pass an empty Set of selected actors. If you pass only the actors you want in the selected actors Set. Only those should be exported in your glTF file.
By default the glTF export should preserve the hierarchy of elements you are exporting. You should be able to check that if you open the glTF in a DCC such as blender.
You can also create a variable of glTFExportOption and edit its options to your needs and pass it to the “Export to glTF” function.