sqlite has r-trees for instance [0]. Could it be good enough for most use cases? If it's to query a knowledge base for instance, a couple dimensions should be sufficient. With the added benefit of being able to query your data in other ways.
Even if you could make it perform well, it would not do what you want.
https://github.com/asg017/sqlite-vss
Not associated with the project, just love SQLite and find it very useful.