Hi again, Dave.
I've already clicked on Force Bass Track To Simple.
"Force bass track to simple" does not have the same effect as the "Force song to simple arrangement" that I mentioned above. The one I mentioned, stops BIAB from introducing chord variations (if the RTs make variations possible).
I've downloaded the SGU file. Thank you for making that available it helps a great deal.
When I generated and played the song, it sounded fine. Also, the particular bass that you use (RT 464) has notation associated with it. If you go to "Notation mode", click on the "B" I've highlighted (#1), you will be able to see the bass's notation. As you can see below, it definitely finished on "D" for me.

For what it is worth, to the best of my knowledge, BIAB has never accepted a slash chord that has a bass that's the same name as the chord root (e.g. Caug/C, D13/D, Am/A, etc.). This would explain why Dm/D does not work for you. BIAB understands the "/D" because of the chord name.
One other thing: I noticed that in the song's ending there were two Dm chords. In the ending position, BIAB only interprets and first chord. The second one would have remained unseen by BIAB. This is normal "ending" behaviour for the program.
Lastly, I noticed that all tracks have notation attached to them. This is great because it helps to see what is happening when the song is playing. When I looked at the Piano track (see image below), it can be seen that the ending notes are F and C. Without bass, this definitely has an "F" sound quality to it. Sitting on top of the D bass, though, the sound is Dm7 sound rather than F (to my ears, at least).

I have a limited understanding of bossanovas but, as far as I can recall, they often end on a version of the tonic 7th chord.
Hope this additional information helps,
Noel