A user with a custom Vault Security Profile that contains the same permissions as a Vault Owner user is not able to perform the same actions as a Vault Owner.
This is working as designed.
The system provided Vault Owner is the only account that can supersede all document sharing and security settings. Users cannot make a copy of the Vault Owner security profile in Vault.
If a user replicates all the permissions exactly, it still will not grant the system provided permissions that Vault Owner has. The ability to edit document settings is only available to Vault Owners and the individuals and groups with the appropriate roles in sharing settings on specific documents and in specific lifecycle states.
The solution is to grant the affected user document-level permissions so that they can perform the necessary document-level actions.
Vault Help Documentation: N/A