Just take the stock Template(s) you want to use. Set the Audio Connections as appropriate. Save this as your own Template & use this to start Empty Projects (or whatever the Template was for).
The Templates that come with Cubase are meant to used as starting points to be customized for each individual’s unique needs. The intention is that you then use these new Templates, customized for your needs, to start Projects. The stock Templates are not meant to be starting points for Projects, they are meant to be the starting point to make Templates that you can then use to start Projects.
In Cubase the Audio Connections configuration is saved at the Project level not the Program level (i.e. there is no “default” configuration for your installation of Cubase). This lets you use different Audio Connection configs for different Projects and even Templates. I have about a half-dozen different Audio Connection Presets I use for Inputs. Template A might use a Connection Preset that is totally different from what Template B uses.