Some of the nextcloud-configuration-options are overwritten by the ‘nethserver-nextcloud-occ-conf’-action.
ex. I want the ‘ldapEmailAttribute’ for AD to be ‘mail’, but after executing the ‘nethserver-nextcloud-occ-conf’-action, it will be ‘userPrincipalName’ again.
IIRC the scripts modify the default nextcloud configuration (named s01). Creating a new configuration from occ command might allow to configure every setting independently of the scripts… but then some of the auto-configuration magic under the hood may not apply.
But what you are describing sounds like a bug or a missing feature.