Most of your work seems over my head, but doesn't the "mammoth" example indicate that by tweaking numbers you can end up getting just about any visual blob you want?
The dimensionality reduction model I used, PaCMAP, had only a single parameter I could tweak, which I did not. However, it is somewhat non-deterministic AFAIK, so the final arrangement can vary on each run, but in my experience, the arrangements tend to look the same, just oriented differently.