There is a very handy extension for generating UUIDs in sqlite: https://sqlite.org/src/file/ext/misc/uuid.c
It would be nice to include it into go-sqlite3 as a loadable extension.
It's actually very small and shouldn't add too much overhead, so it could also be loaded per default.

I did not really understand how the upgrade tool pulls in extensions, or how I would add the extension there.

As an alternative, one can create a new instance of the driver with a go implementation. I successfully made that work, but it was basically impossible to use with other libraries like ORMs due to the self-initialization nature of the go SQL drivers.