Some parts of the completion system for nrfutil toolchain-manager are based on the current configuration options set by the user (controlled using the config subcommand). These options can, for any relevant command, be overridden using a corresponding flag. For example, the install-dir configuration variable can be overridden using the --install-dir flag. The overridden value will not be picked up by the completion system (since it's based on the current config options), meaning the values given by the completion system are likely going to be wrong.
If you rely on the completion system, it is therefore recommended to use the config subcommand to update the configuration variables instead of using the override flags. The override flags are more useful in scripts (where updating the config may be unfeasible) or if the value is only changed for a brief time.