Thank you for your post and I apologize for the delayed response!
From the AzureAD side, the best way to get the individual VM metrics of each customer, is by utilizing the Azure Compute REST APIs as you mentioned within your post. When it comes to the app being registered within the Partner Center, I've added the partner-center-api tag to this thread so their community can take a closer look into your issue.
If you have any other questions, please let me know.
Thank you for your time and patience throughout this issue.
Please remember to "Accept Answer" if any answer/reply helped, so that others in the community facing similar issues can easily find the solution.