Entra ID App Provisioning does not support custom SCIM attributes that are complex or multi-valued. They can generally be supported for gallery applications with custom SCIM-based provisioning connectors built into the Enterprise Application, but are not supported for custom attributes added manually to the schema of provisioning jobs.
This is publicly documented here: https://learn.microsoft.com/en-us/entra/identity/app-provisioning/customize-application-attributes#provisioning-a-custom-extension-attribute-to-a-scim-compliant-application
Custom attributes can't be referential attributes, multi-value, or complex-typed attributes. Custom multi-value and complex-typed extension attributes are currently supported only for applications in the gallery.