Cheers,
Anlv

let me clarify things first a bit.

Reproduce:

1. You have a scene A in an alien scene format such as FBX or OBJ.
2. You have an existing native Cinema 4D scene B.
3. You are trying to merge A into B.

Result:
The objects of A appear before the objects of B in the scene hierarchy of the merged scene. Even when you change the insertion order in Preferences > Interface.

First of all, it is not very surprising that "insert at" does not work (and "paste at" does neither), because these are for individual objects within a scene, not for merging entire scenes. What you are effectively missing is a scene merge order option and this does not really have something to do with importers. This would be addressed best by a feature request in our Support Center.

With a pinch of Python, you can solve this yourself as demonstrated by @Anlv (thanks!). Using BaseList2D.GetGUID as @Anlv did is okay, but the more native solution would be hash(obj), i.e., C4DAtom.__hash__. Scene elements are for quite a while now natively hashable, so you can for example do this:

roots: set[int] = { hash(obj) for obj in doc.GetObjects() }
new_roots: set[int] = roots.intersection({ hash(obj) for obj in new_doc.GetObjects() })

And it will give you the set of all root level hashes (GeMarker IDs). I think also the transform copying @Anlv does at the end of the script should not be necessary, because these are root level objects, and therefore removing and re-adding them will not affect their transforms (as they have no parents to which their transform would be relative to). But I have not run @Anlv's full script myself, so it could be that I am overlooking something.

Cheers,
Ferdinand

Hope this helps.
Here is another example that can directly execute the import

import c4d

def main():
    doc = c4d.documents.GetActiveDocument()
    path = c4d.storage.LoadDialog(
        c4d.FILESELECTTYPE_SCENES,
        "Import Scene"
    )
    if not path:
        return

    roots = doc.GetObjects()
    anchor = roots[-1] if roots else None
    old_guids = {obj.GetGUID() for obj in roots}

    flags = (
        c4d.SCENEFILTER_OBJECTS |
        c4d.SCENEFILTER_MATERIALS |
        c4d.SCENEFILTER_MERGESCENE |
        c4d.SCENEFILTER_DIALOGSALLOWED
    )

    c4d.StopAllThreads()
    doc.StartUndo()

    try:
        doc.AddUndo(c4d.UNDOTYPE_CHANGE, doc)

        if not c4d.documents.MergeDocument(doc, path, flags, None):
            c4d.gui.MessageDialog("Import failed.")
            return

        # Find the newly imported root objects.
        imported = [
            obj for obj in doc.GetObjects()
            if obj.GetGUID() not in old_guids
        ]

        # Move them below the previous last root object.
        if anchor:
            for obj in imported:
                matrix = obj.GetMg()
                doc.AddUndo(c4d.UNDOTYPE_CHANGE, obj)
                obj.Remove()
                obj.InsertAfter(anchor)
                obj.SetMg(matrix)
                anchor = obj
    finally:
        doc.EndUndo()
        c4d.EventAdd()

if __name__ == "__main__":
    main()

Cheers,
Anlv