FWIW, I tested this but with Groove Agent 5 (the full version, not the SE one), as I don’t have SD3 at disposal, to see if the same issue could occur with a different drums VSTi of nearly the same kind. Repro :
-
[right-clic] > Add track > Instrument → Groove Agent
-
In the Right Zone > VSTi > Track Instruments panel, I used the Input/Output Options of Groove Agent to add 4 output busses.
-
In the GA5 UI, I routed individual instruments of the bundled Beat Agent-Ambiant Kit 2 to different outputs created at the previous step, made a drag&drop of an available pattern to the main GA5 instrument track in Cubase and duplicated it two times.
-
File > Export > Audio Mixdown. I selected the different GA5 outputs, using the Multiple option and started the related export queue.
-
Result is this one :
As shown, I can freely move each resulting audio track anywhere in the track list. So, it seems that the eventual issue is rather on the SD3 side than on Cubase one, unless I haven’t got the real issue at hand.
What I don’t get is that there is a Superior Drummer 3 subfolder in the Cubase default Rack Instruments one in your last screenshot, though you have said using SD3 as a track instrument in your repro above, while evoking a SD3 ‘containing folder’ : there is no default ‘containing folder’ created when using a track instrument.
So, are you using two instances of SD3, one as ‘track’ and one as ‘rack’ ? Maybe the issue comes from there. Otherwise, there are still clarifications needed… 
EDIT : prolonging the test, I tried again with GA5, but this time, as a rack instrument. So, the exact same repro excepting that I used directly the right zone to add a rack instrument for Groove Agent, creating in the process an associated MIDI track when prompted about it.
Cubase behavior is the same, the audio tracks being created and placed just below the associated MIDI track, thus, outside the Groove Agent default containing folder. I can then again freely move each of them as wanted.
EDIT 2 : at a point, I’ve been wondering if the issue wasn’t correlated to the fact that the instrument track was the only track in the project, beside the audio mixdown ones. So, I created an empty project and immediatly add GA5 as a track instrument to check this.
It’s not the case. I can also freely move the audio tracks but with a logical restriction : I cannot place any of them as a ‘subtrack’ of the existing related instrument track. The only thing I can do, in this case, is to move resulting mixdown audio track(s) above it.
Cubase Pro 15.0.10