thanks for your post, and sorry for the trouble.
Sorry, I have not yet looked into that, so that I can’t help with this.
Note that just adding a Custom Taxonomy is likely not sufficient, as TablePress does not use the native user interface for managing tables. It essentially only uses them to store the data.
I think Taxonomy for manage Tables is a good new feature.
I hope in the future your plugin have it.
I do have some ideas for things like categories, but I’m not sure yet if I will be using the taxonomy feature in WordPress to implement it.
I think should be use Custom Taxonomy of WordPress Core. Because it’s have many base feature from WordPress Core.