mrnemesys I doubt this can be achieved via an extension, but if you fork core you have a few possibilities.
This thread is a good start: https://stackoverflow.com/a/28589029/3133038
Either create a different database connection without prefix and set the User model to use that.
Or update Flarum's AbstractModel to manually change every model table name to include the prefix manually except for User, and do not specify the prefix in the database connection.
You could also maybe consider using a (prefixed) database view to have a single table across your app, or keep two different tables, login via a login provider and manually sync the data you need between the two.