Hey Michael,
I was able to reproduce the behaviour with a really simple self-made model, which I can obviously share with you:
https://mega.nz/file/Rlwk3YRS#CvjDmf1PGjySmlty61QD5qLHD7dXzG4gecF8rlpY7HY
I created two cubes in FreeCAD, which do not touch.
Afterwards I fusioned both of them and exported a STEP file.
Both cubes, although completely separated from another, are coming up as one object in MoI.
Nevertheless, I dont think there is great need to improve this, I can just select the sub-object and rename it - done.
P.S.:
This opens up a whole new topic and I am not sure if you even want to hear it, but I really do not trust your Separate / Join commands.
I import the step files into Cinema 4D after I am done in MoI and all objects I used these commands on have one or another problem.
These range from empty objects (there are no faces / edges in the objects, although their names appear in the object list in C4D),
to broken boolean operations, where all of a sudden I can see the original boolean objects and the booleans, which looked fine in MoI, are incomplete all of a sudden.
So I tend to avoid them until now.
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