Work 365 does support Microsoft Azure Stack.

To provision Azure Stack in Work 365, you would provision ‘Microsoft Azure’ as a regular subscription from the product catalog. Once the regular Azure subscription is provisioned with Partner Center, Partners would then need to connect with Microsoft to receive approval to make the regular Azure subscription an Azure Stack subscription. Once approved, Microsoft will make the Azure subscription an Azure Stack Subscription. 

Consumption then for Azure stack will be labeled as Azure Stack. Just like regular Azure consumption, the usage summary will be provided by the Microsoft provider invoice, and the usage details will be provided through the customer’s tenant. See Work 365 Usage Subscriptions and provider invoices for details.

Lastly, Work 365 will invoice Azure stack consumption just like a regular Azure subscription. The usage summary will be captured in the invoice as a single cost line item including the subscription markup %. Then the usage details will be available in the CSV file attachment to the Work 365 invoice. Note: Usage details do not impact the calculated cost of Azure in the actual invoice. See a Work 365 invoicing overview for details.