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It's currently not possible to configure "Override Win32 application options" at the product nor vendor level for Custom Apps with the Publisher. Kindly allow this to be configurable for customers.
For example: if a customer wanted to maintain a Custom App's dependency relationship with other Win32 packages in Intune, their only option is to configure this via the Options window - thus impacting the configuration for all apps and updates, and forcing them to inverse their existing configuration where currently applied at the product or vendor level.
Thanks Adam!