This can be achieved with the Partner Generated Billing - Include Tags functionality.
At the Partner level, under the Setup > Admin > Settings > Partner Billing section, you can find an 'Include Tags' feature:
If you wish to pass down the Cost Allocation tags to the customer-level bills that are generated by the Partner Billing engine, this feature must be enabled.
This would allow your customers to use the Cost Allocation tags within the FlexReports feature.