The problem with missing options came from config/packages/doctrine.yaml

There, the standard config sets options that were removed in doctrine-orm v3, namely:

doctrine.dbal.use_savepoints
doctrine.orm.auto_generate_proxy_classes
doctrine.orm.enable_lazy_ghost_objects
doctrine.orm.report_fields_where_declared

Commenting out / removing those options resolved the issue.
Hopefully the package supplying those config options fixes this. In the meantime, manually editing the file seems to work.